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/7dnj_30785.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb" } resolution = 3.3 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= 0.119 sd= 0.276 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 8 5.16 5 C 1736 2.51 5 N 472 2.21 5 O 535 1.98 5 H 2800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5551 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3184 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1174 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 0.96, per 1000 atoms: 0.17 Number of scatterers: 5551 At special positions: 0 Unit cell: (67.925, 71.06, 110.77, 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 8 16.00 O 535 8.00 N 472 7.00 C 1736 6.00 H 2800 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: 1.19 Conformation dependent library (CDL) restraints added in 162.3 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 50.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.570A pdb=" N SER A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.582A pdb=" N ALA A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.893A pdb=" N TYR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 128 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 140 removed outlier: 5.080A pdb=" N ASP A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.760A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.500A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.502A pdb=" N GLN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'H' and resid 23 through 33 Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 56 through 59 No H-bonds generated for 'chain 'H' and resid 56 through 59' Processing sheet with id= A, first strand: chain 'E' and resid 12 through 16 removed outlier: 3.522A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.721A pdb=" N ILE H 3 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER H 65 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS H 6 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU H 67 " --> pdb=" O LYS H 6 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 333 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: 0.96 Time building geometry restraints manager: 1.36 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: 2798 1.14 - 1.31: 487 1.31 - 1.47: 1016 1.47 - 1.64: 1275 1.64 - 1.80: 14 Bond restraints: 5590 Sorted by residual: bond pdb=" NE2 GLN E 49 " pdb="HE21 GLN E 49 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N LEU E 67 " pdb=" H LEU E 67 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N ILE E 13 " pdb=" H ILE E 13 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" NE ARG A 93 " pdb=" HE ARG A 93 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ALA A 110 " pdb=" H ALA A 110 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 5585 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.82: 85 106.82 - 113.59: 6828 113.59 - 120.36: 1789 120.36 - 127.13: 1425 127.13 - 133.90: 24 Bond angle restraints: 10151 Sorted by residual: angle pdb=" N GLY A 54 " pdb=" CA GLY A 54 " pdb=" C GLY A 54 " ideal model delta sigma weight residual 112.65 115.10 -2.45 1.30e+00 5.92e-01 3.56e+00 angle pdb=" C SER A 53 " pdb=" N GLY A 54 " pdb=" CA GLY A 54 " ideal model delta sigma weight residual 121.87 118.84 3.03 1.64e+00 3.72e-01 3.42e+00 angle pdb=" N GLY H 35 " pdb=" CA GLY H 35 " pdb=" C GLY H 35 " ideal model delta sigma weight residual 113.18 116.85 -3.67 2.37e+00 1.78e-01 2.39e+00 angle pdb=" C VAL E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta sigma weight residual 122.93 120.74 2.19 1.45e+00 4.76e-01 2.28e+00 angle pdb=" C GLU H 64 " pdb=" CA GLU H 64 " pdb=" CB GLU H 64 " ideal model delta sigma weight residual 111.80 109.78 2.02 1.46e+00 4.69e-01 1.91e+00 ... (remaining 10146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 2317 15.91 - 31.81: 191 31.81 - 47.72: 41 47.72 - 63.62: 29 63.62 - 79.53: 6 Dihedral angle restraints: 2584 sinusoidal: 1470 harmonic: 1114 Sorted by residual: dihedral pdb=" CB LYS E 33 " pdb=" CG LYS E 33 " pdb=" CD LYS E 33 " pdb=" CE LYS E 33 " ideal model delta sinusoidal sigma weight residual -60.00 -116.56 56.56 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA GLN H 41 " pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " pdb=" CD GLN H 41 " ideal model delta sinusoidal sigma weight residual 60.00 113.52 -53.52 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA GLN H 41 " pdb=" C GLN H 41 " pdb=" N ARG H 42 " pdb=" CA ARG H 42 " ideal model delta harmonic sigma weight residual 180.00 165.24 14.76 0 5.00e+00 4.00e-02 8.71e+00 ... (remaining 2581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.056: 110 0.056 - 0.084: 36 0.084 - 0.112: 15 0.112 - 0.140: 8 Chirality restraints: 441 Sorted by residual: chirality pdb=" CA ILE E 44 " pdb=" N ILE E 44 " pdb=" C ILE E 44 " pdb=" CB ILE E 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE H 36 " pdb=" N ILE H 36 " pdb=" C ILE H 36 " pdb=" CB ILE H 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE E 13 " pdb=" N ILE E 13 " pdb=" C ILE E 13 " pdb=" CB ILE E 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 438 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 30 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 122 " 0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 123 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 37 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.51e-01 pdb=" N PRO E 38 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.011 5.00e-02 4.00e+02 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 453 2.14 - 2.76: 10394 2.76 - 3.37: 16013 3.37 - 3.99: 21305 3.99 - 4.60: 31691 Nonbonded interactions: 79856 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 23 " pdb=" OE1 GLU A 60 " model vdw 1.530 1.850 nonbonded pdb=" H3 MET H 1 " pdb=" O VAL H 17 " model vdw 1.543 1.850 nonbonded pdb=" O ASP E 21 " pdb=" HG1 THR E 55 " model vdw 1.549 1.850 nonbonded pdb=" O ILE H 36 " pdb="HE22 GLN H 41 " model vdw 1.609 1.850 nonbonded pdb=" O THR E 14 " pdb=" HZ1 LYS E 33 " model vdw 1.616 1.850 ... (remaining 79851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name \ HH22)))) selection = (chain 'H' and resid 1 through 72) } 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=0.49 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: 0.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 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:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:4.260 Internal consistency checks: 0.000 Total: 12.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.025 2790 Z= 0.183 Angle : 0.555 4.394 3774 Z= 0.303 Chirality : 0.039 0.140 441 Planarity : 0.004 0.029 490 Dihedral : 13.883 79.531 1076 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.65 % Allowed : 2.27 % Favored : 97.09 % 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: -2.12 (0.43), residues: 336 helix: -1.92 (0.34), residues: 172 sheet: -0.85 (0.77), residues: 51 loop : -0.35 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 42 TYR 0.006 0.001 TYR A 13 PHE 0.011 0.001 PHE A 107 TRP 0.004 0.001 TRP A 75 HIS 0.004 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.158 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: A 29 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 81 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 146 ILE cc_start: 0.8660 (tp) cc_final: 0.8365 (tp) REVERT: H 2 GLN cc_start: 0.8497 (tp40) cc_final: 0.8277 (tp40) REVERT: H 49 GLN cc_start: 0.8383 (tt0) cc_final: 0.7911 (tm-30) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.1683 time to fit residues: 24.9628 Evaluate side-chains 107 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 122 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2790 Z= 0.269 Angle : 0.562 4.216 3774 Z= 0.303 Chirality : 0.041 0.162 441 Planarity : 0.003 0.027 490 Dihedral : 6.199 46.320 371 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.94 % Allowed : 9.71 % Favored : 88.35 % 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: -0.98 (0.45), residues: 336 helix: -0.80 (0.38), residues: 171 sheet: -0.90 (0.76), residues: 52 loop : 0.16 (0.57), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 54 TYR 0.010 0.001 TYR A 25 PHE 0.014 0.001 PHE A 107 TRP 0.003 0.001 TRP A 75 HIS 0.005 0.002 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.252 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: A 98 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 156 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7473 (tm-30) REVERT: H 25 ASN cc_start: 0.9137 (m110) cc_final: 0.8881 (m110) REVERT: H 49 GLN cc_start: 0.8391 (tt0) cc_final: 0.7987 (tm-30) outliers start: 6 outliers final: 4 residues processed: 117 average time/residue: 0.2968 time to fit residues: 40.6037 Evaluate side-chains 110 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain H residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2790 Z= 0.208 Angle : 0.547 6.671 3774 Z= 0.291 Chirality : 0.040 0.152 441 Planarity : 0.003 0.025 490 Dihedral : 5.998 47.728 371 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.29 % Allowed : 14.56 % Favored : 84.14 % 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: -0.55 (0.45), residues: 336 helix: -0.36 (0.39), residues: 171 sheet: -0.70 (0.75), residues: 51 loop : 0.19 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.014 0.001 TYR A 25 PHE 0.013 0.001 PHE A 107 TRP 0.002 0.000 TRP A 75 HIS 0.005 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.176 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: A 98 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6912 (mp0) REVERT: A 156 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7439 (tm-30) REVERT: H 25 ASN cc_start: 0.9105 (m110) cc_final: 0.8845 (m110) REVERT: H 49 GLN cc_start: 0.8372 (tt0) cc_final: 0.7971 (tm-30) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.2232 time to fit residues: 29.3257 Evaluate side-chains 110 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2790 Z= 0.249 Angle : 0.561 6.608 3774 Z= 0.298 Chirality : 0.040 0.165 441 Planarity : 0.004 0.025 490 Dihedral : 5.969 57.797 371 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.59 % Allowed : 15.86 % Favored : 81.55 % 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: -0.27 (0.45), residues: 336 helix: -0.15 (0.39), residues: 171 sheet: -0.31 (0.78), residues: 48 loop : 0.19 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 48 TYR 0.005 0.001 TYR H 59 PHE 0.013 0.002 PHE E 4 TRP 0.002 0.001 TRP A 177 HIS 0.005 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 156 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 15 LEU cc_start: 0.9021 (mt) cc_final: 0.8810 (mt) REVERT: H 25 ASN cc_start: 0.9085 (m110) cc_final: 0.8753 (m110) outliers start: 8 outliers final: 6 residues processed: 109 average time/residue: 0.1772 time to fit residues: 22.7209 Evaluate side-chains 107 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN E 2 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2790 Z= 0.222 Angle : 0.564 5.894 3774 Z= 0.296 Chirality : 0.040 0.151 441 Planarity : 0.003 0.027 490 Dihedral : 5.741 58.007 371 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.27 % Allowed : 18.12 % Favored : 79.61 % 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: -0.07 (0.45), residues: 336 helix: 0.10 (0.40), residues: 171 sheet: -0.29 (0.79), residues: 48 loop : 0.15 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 149 TYR 0.014 0.001 TYR A 13 PHE 0.013 0.002 PHE E 4 TRP 0.002 0.001 TRP A 177 HIS 0.005 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 156 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 25 ASN cc_start: 0.9061 (m110) cc_final: 0.8588 (m110) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.1447 time to fit residues: 18.0922 Evaluate side-chains 105 residues out of total 309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.0010 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 2 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2790 Z= 0.221 Angle : 0.572 7.085 3774 Z= 0.300 Chirality : 0.040 0.146 441 Planarity : 0.004 0.028 490 Dihedral : 5.657 57.014 371 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.59 % Allowed : 18.12 % Favored : 79.29 % 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: 0.15 (0.45), residues: 336 helix: 0.28 (0.40), residues: 170 sheet: -0.15 (0.80), residues: 48 loop : 0.25 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 149 TYR 0.005 0.001 TYR A 13 PHE 0.013 0.001 PHE E 4 TRP 0.002 0.001 TRP A 177 HIS 0.005 0.001 HIS A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 626.63 seconds wall clock time: 11 minutes 11.75 seconds (671.75 seconds total)