Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.62 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7pcq_13325.pdb" } resolution = 3.62 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1409 2.51 5 N 382 2.21 5 O 395 1.98 5 H 2189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2145 Classifications: {'peptide': 141} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2236 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 0.84, per 1000 atoms: 0.19 Number of scatterers: 4381 At special positions: 0 Unit cell: (58.68, 61.94, 68.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 395 8.00 N 382 7.00 C 1409 6.00 H 2189 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 138.1 milliseconds 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 534 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 5.916A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.936A pdb=" N MET A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 73 through 79' Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.758A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.956A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 58 through 76 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.525A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLU B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 146 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2186 1.14 - 1.31: 360 1.31 - 1.48: 910 1.48 - 1.65: 974 1.65 - 1.81: 9 Bond restraints: 4439 Sorted by residual: bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N ALA B 62 " pdb=" H ALA B 62 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" N SER A 84 " pdb=" H SER A 84 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N VAL A 93 " pdb=" H VAL A 93 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" N TYR B 35 " pdb=" H TYR B 35 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 4434 not shown) Histogram of bond angle deviations from ideal: 100.96 - 107.55: 246 107.55 - 114.14: 5234 114.14 - 120.73: 1488 120.73 - 127.32: 1044 127.32 - 133.91: 38 Bond angle restraints: 8050 Sorted by residual: angle pdb=" N GLY A 18 " pdb=" CA GLY A 18 " pdb=" C GLY A 18 " ideal model delta sigma weight residual 110.77 115.07 -4.30 1.93e+00 2.68e-01 4.97e+00 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 110.70 112.49 -1.79 1.22e+00 6.72e-01 2.15e+00 angle pdb=" CA PRO B 124 " pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 117.93 119.33 -1.40 1.20e+00 6.94e-01 1.37e+00 angle pdb=" C THR A 118 " pdb=" N PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 125.00 129.46 -4.46 4.10e+00 5.95e-02 1.18e+00 angle pdb=" C PRO B 124 " pdb=" N PRO B 125 " pdb=" CD PRO B 125 " ideal model delta sigma weight residual 125.00 129.38 -4.38 4.10e+00 5.95e-02 1.14e+00 ... (remaining 8045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 1932 15.73 - 31.47: 95 31.47 - 47.20: 40 47.20 - 62.94: 31 62.94 - 78.67: 1 Dihedral angle restraints: 2099 sinusoidal: 1097 harmonic: 1002 Sorted by residual: dihedral pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " ideal model delta sinusoidal sigma weight residual -60.00 -116.32 56.32 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CA ARG B 40 " pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N PHE A 46 " pdb=" CA PHE A 46 " pdb=" CB PHE A 46 " pdb=" CG PHE A 46 " ideal model delta sinusoidal sigma weight residual -60.00 -102.13 42.13 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 2096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 222 0.022 - 0.044: 77 0.044 - 0.066: 19 0.066 - 0.088: 26 0.088 - 0.109: 6 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA PRO B 36 " pdb=" N PRO B 36 " pdb=" C PRO B 36 " pdb=" CB PRO B 36 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" C PRO A 77 " pdb=" CB PRO A 77 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.10e-01 ... (remaining 347 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 124 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 35 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.02e-01 pdb=" N PRO B 36 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 3 " -0.014 5.00e-02 4.00e+02 2.13e-02 7.27e-01 pdb=" N PRO A 4 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " -0.012 5.00e-02 4.00e+02 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 432 2.24 - 2.83: 9240 2.83 - 3.42: 12399 3.42 - 4.01: 15834 4.01 - 4.60: 24530 Nonbonded interactions: 62435 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" H HIS A 122 " model vdw 1.647 1.850 nonbonded pdb=" HE1 TRP A 14 " pdb=" OG1 THR A 67 " model vdw 1.651 1.850 nonbonded pdb=" O THR B 4 " pdb=" H LYS B 8 " model vdw 1.670 1.850 nonbonded pdb=" OE1 GLU A 27 " pdb=" HE2 HIS A 112 " model vdw 1.779 1.850 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.787 2.100 ... (remaining 62430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:3.330 Internal consistency checks: 0.000 Total: 10.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 2250 Z= 0.152 Angle : 0.442 4.460 3061 Z= 0.241 Chirality : 0.032 0.109 350 Planarity : 0.003 0.028 391 Dihedral : 10.870 78.670 784 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.46), residues: 283 helix: 1.71 (0.32), residues: 220 sheet: None (None), residues: 0 loop : 0.79 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.003 0.001 TYR B 145 PHE 0.006 0.001 PHE A 46 TRP 0.004 0.001 TRP A 14 HIS 0.002 0.001 HIS B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.9000 (tttm) cc_final: 0.8371 (tttm) REVERT: A 47 ASP cc_start: 0.7863 (t0) cc_final: 0.7609 (t0) REVERT: B 37 TRP cc_start: 0.8566 (p90) cc_final: 0.6965 (t60) REVERT: B 102 ASN cc_start: 0.9011 (m-40) cc_final: 0.8730 (m110) REVERT: B 127 GLN cc_start: 0.9128 (tt0) cc_final: 0.8555 (tm-30) REVERT: B 131 GLN cc_start: 0.8950 (mm110) cc_final: 0.8485 (mm110) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1496 time to fit residues: 29.4153 Evaluate side-chains 138 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2250 Z= 0.211 Angle : 0.533 4.498 3061 Z= 0.279 Chirality : 0.036 0.118 350 Planarity : 0.003 0.029 391 Dihedral : 5.421 71.594 299 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 23.38 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.48), residues: 283 helix: 2.40 (0.33), residues: 222 sheet: None (None), residues: 0 loop : 1.07 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.006 0.001 TYR A 24 PHE 0.011 0.001 PHE A 36 TRP 0.007 0.001 TRP A 14 HIS 0.003 0.001 HIS B 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8604 (tt0) cc_final: 0.8248 (tt0) REVERT: A 68 ASN cc_start: 0.9014 (t0) cc_final: 0.8609 (t0) REVERT: A 72 HIS cc_start: 0.9064 (m90) cc_final: 0.8733 (m90) REVERT: A 94 ASP cc_start: 0.8342 (t0) cc_final: 0.8045 (t0) REVERT: B 35 TYR cc_start: 0.8896 (m-80) cc_final: 0.8663 (m-80) REVERT: B 37 TRP cc_start: 0.8700 (p90) cc_final: 0.6833 (t60) REVERT: B 57 ASN cc_start: 0.8085 (t0) cc_final: 0.7881 (t0) REVERT: B 94 ASP cc_start: 0.8778 (m-30) cc_final: 0.8232 (p0) REVERT: B 108 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8720 (t0) REVERT: B 127 GLN cc_start: 0.9178 (tt0) cc_final: 0.8623 (tm-30) REVERT: B 131 GLN cc_start: 0.9041 (mm110) cc_final: 0.8665 (mm110) outliers start: 6 outliers final: 3 residues processed: 156 average time/residue: 0.2690 time to fit residues: 48.0449 Evaluate side-chains 147 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 108 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.0070 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2250 Z= 0.183 Angle : 0.532 4.137 3061 Z= 0.269 Chirality : 0.037 0.142 350 Planarity : 0.003 0.031 391 Dihedral : 5.078 62.900 299 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.46 % Allowed : 28.57 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.50), residues: 283 helix: 2.61 (0.34), residues: 221 sheet: None (None), residues: 0 loop : 1.42 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.002 0.001 TYR B 130 PHE 0.014 0.001 PHE A 117 TRP 0.006 0.001 TRP A 14 HIS 0.003 0.001 HIS B 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8998 (t0) cc_final: 0.8775 (t0) REVERT: A 94 ASP cc_start: 0.8318 (t0) cc_final: 0.8101 (t0) REVERT: B 35 TYR cc_start: 0.8929 (m-80) cc_final: 0.8655 (m-80) REVERT: B 37 TRP cc_start: 0.8716 (p90) cc_final: 0.6754 (t60) REVERT: B 127 GLN cc_start: 0.9128 (tt0) cc_final: 0.8607 (tm-30) REVERT: B 131 GLN cc_start: 0.8983 (mm110) cc_final: 0.8724 (mm110) outliers start: 8 outliers final: 7 residues processed: 148 average time/residue: 0.2020 time to fit residues: 34.1021 Evaluate side-chains 147 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2250 Z= 0.176 Angle : 0.545 4.479 3061 Z= 0.278 Chirality : 0.038 0.160 350 Planarity : 0.004 0.031 391 Dihedral : 4.539 48.886 299 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.90 % Allowed : 32.03 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.51), residues: 283 helix: 2.73 (0.35), residues: 221 sheet: None (None), residues: 0 loop : 1.45 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.003 0.001 TYR B 145 PHE 0.016 0.001 PHE A 117 TRP 0.007 0.001 TRP A 14 HIS 0.007 0.001 HIS A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASN cc_start: 0.9012 (t0) cc_final: 0.8621 (t0) REVERT: A 72 HIS cc_start: 0.9072 (m90) cc_final: 0.8754 (m90) REVERT: B 61 LYS cc_start: 0.9032 (mttt) cc_final: 0.8795 (ptpp) REVERT: B 94 ASP cc_start: 0.8778 (m-30) cc_final: 0.8179 (p0) REVERT: B 98 VAL cc_start: 0.9432 (t) cc_final: 0.9139 (p) REVERT: B 127 GLN cc_start: 0.9076 (tt0) cc_final: 0.8653 (tm-30) REVERT: B 131 GLN cc_start: 0.9078 (mm110) cc_final: 0.8878 (mm110) outliers start: 9 outliers final: 6 residues processed: 154 average time/residue: 0.1722 time to fit residues: 30.5048 Evaluate side-chains 150 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2250 Z= 0.188 Angle : 0.604 6.422 3061 Z= 0.301 Chirality : 0.039 0.167 350 Planarity : 0.004 0.030 391 Dihedral : 4.230 36.666 299 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.73 % Allowed : 37.66 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.50), residues: 283 helix: 2.57 (0.33), residues: 221 sheet: None (None), residues: 0 loop : 1.17 (0.91), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.020 0.002 TYR B 35 PHE 0.020 0.002 PHE B 85 TRP 0.007 0.001 TRP A 14 HIS 0.013 0.001 HIS A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 566 Ramachandran restraints generated. 283 Oldfield, 0 Emsley, 283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8587 (tt0) cc_final: 0.8282 (tt0) REVERT: A 68 ASN cc_start: 0.9037 (t0) cc_final: 0.8805 (t0) REVERT: B 94 ASP cc_start: 0.8802 (m-30) cc_final: 0.8207 (p0) REVERT: B 127 GLN cc_start: 0.9088 (tt0) cc_final: 0.8658 (tm-30) outliers start: 4 outliers final: 4 residues processed: 141 average time/residue: 0.1412 time to fit residues: 22.8678 Evaluate side-chains 141 residues out of total 231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 20.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.8230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2250 Z= 0.207 Angle : 0.645 6.400 3061 Z= 0.333 Chirality : 0.040 0.150 350 Planarity : 0.004 0.040 391 Dihedral : 4.217 28.100 299 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 41.99 % Favored : 56.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.50), residues: 283 helix: 2.34 (0.33), residues: 220 sheet: None (None), residues: 0 loop : 1.28 (0.89), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 104 TYR 0.011 0.001 TYR B 35 PHE 0.019 0.002 PHE B 85 TRP 0.005 0.001 TRP A 14 HIS 0.015 0.001 HIS A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 608.64 seconds wall clock time: 10 minutes 53.68 seconds (653.68 seconds total)