Starting phenix.real_space_refine on Sun May 19 16:30:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.0 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/5yi5_6830.map" } resolution = 3.0 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= 0.056 sd= 0.130 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 7 5.16 5 C 886 2.51 5 N 248 2.21 5 O 273 1.98 5 H 1360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 133": "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: 2774 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2774 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Time building chain proxies: 0.60, per 1000 atoms: 0.22 Number of scatterers: 2774 At special positions: 0 Unit cell: (72.6596, 62.8785, 58.6866, 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 7 16.00 O 273 8.00 N 248 7.00 C 886 6.00 H 1360 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: 0.50 Conformation dependent library (CDL) restraints added in 81.7 milliseconds 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 41 removed outlier: 3.737A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 76 removed outlier: 3.560A pdb=" N LYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 124 removed outlier: 3.580A pdb=" N ASN A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.951A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.517A pdb=" N LYS A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) 90 hydrogen bonds defined for protein. 270 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: 0.41 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 1357 1.14 - 1.31: 253 1.31 - 1.48: 567 1.48 - 1.64: 615 1.64 - 1.81: 11 Bond restraints: 2803 Sorted by residual: bond pdb=" N ASP A 151 " pdb=" H ASP A 151 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N GLY A 97 " pdb=" H GLY A 97 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" ND2 ASN A 22 " pdb="HD21 ASN A 22 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N HIS A 106 " pdb=" H HIS A 106 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" N LYS A 69 " pdb=" H LYS A 69 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.59e+01 ... (remaining 2798 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.64: 31 106.64 - 113.47: 3234 113.47 - 120.29: 950 120.29 - 127.12: 814 127.12 - 133.95: 15 Bond angle restraints: 5044 Sorted by residual: angle pdb=" C VAL A 9 " pdb=" CA VAL A 9 " pdb=" CB VAL A 9 " ideal model delta sigma weight residual 111.37 108.75 2.62 1.68e+00 3.54e-01 2.43e+00 angle pdb=" N GLU A 95 " pdb=" CA GLU A 95 " pdb=" C GLU A 95 " ideal model delta sigma weight residual 110.80 113.75 -2.95 2.13e+00 2.20e-01 1.91e+00 angle pdb=" C TYR A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta sigma weight residual 120.28 118.72 1.56 1.34e+00 5.57e-01 1.36e+00 angle pdb=" N ASN A 51 " pdb=" CA ASN A 51 " pdb=" C ASN A 51 " ideal model delta sigma weight residual 111.71 113.04 -1.33 1.15e+00 7.56e-01 1.34e+00 angle pdb=" C ASP A 151 " pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 110.79 112.69 -1.90 1.66e+00 3.63e-01 1.31e+00 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 1261 16.31 - 32.63: 34 32.63 - 48.94: 8 48.94 - 65.25: 8 65.25 - 81.56: 4 Dihedral angle restraints: 1315 sinusoidal: 703 harmonic: 612 Sorted by residual: dihedral pdb=" CA THR A 136 " pdb=" C THR A 136 " pdb=" N HIS A 137 " pdb=" CA HIS A 137 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP A 94 " pdb=" C TRP A 94 " pdb=" N GLU A 95 " pdb=" CA GLU A 95 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LEU A 49 " pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta harmonic sigma weight residual -180.00 -165.42 -14.58 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 1312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 130 0.024 - 0.047: 52 0.047 - 0.071: 15 0.071 - 0.095: 4 0.095 - 0.118: 3 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 201 not shown) Planarity restraints: 425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 17 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C SER A 17 " 0.021 2.00e-02 2.50e+03 pdb=" O SER A 17 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 151 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ASP A 151 " 0.018 2.00e-02 2.50e+03 pdb=" O ASP A 151 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS A 152 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 21 " -0.005 2.00e-02 2.50e+03 9.26e-03 8.57e-01 pdb=" C ILE A 21 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 22 " -0.005 2.00e-02 2.50e+03 ... (remaining 422 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 133 2.19 - 2.79: 5154 2.79 - 3.39: 7064 3.39 - 4.00: 8728 4.00 - 4.60: 13368 Nonbonded interactions: 34447 Sorted by model distance: nonbonded pdb=" HH TYR A 41 " pdb=" OD1 ASP A 93 " model vdw 1.583 1.850 nonbonded pdb=" O HIS A 106 " pdb="HD22 ASN A 110 " model vdw 1.633 1.850 nonbonded pdb=" O GLY A 79 " pdb="HH11 ARG A 80 " model vdw 1.662 1.850 nonbonded pdb=" OE1 GLU A 163 " pdb=" H GLU A 163 " model vdw 1.670 1.850 nonbonded pdb=" HH TYR A 35 " pdb=" OE2 GLU A 108 " model vdw 1.678 1.850 ... (remaining 34442 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=0.51 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: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:4.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:1.980 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 0.013 1443 Z= 0.163 Angle : 0.447 3.697 1944 Z= 0.268 Chirality : 0.031 0.118 204 Planarity : 0.003 0.016 257 Dihedral : 10.142 81.563 543 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.39 (0.57), residues: 170 helix: 0.04 (0.40), residues: 126 sheet: None (None), residues: 0 loop : -0.74 (0.90), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.004 0.001 TYR A 169 PHE 0.005 0.001 PHE A 52 TRP 0.005 0.001 TRP A 94 HIS 0.003 0.001 HIS A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6378 (tm-30) REVERT: A 64 ARG cc_start: 0.8564 (ttt90) cc_final: 0.8232 (tmm-80) REVERT: A 71 MET cc_start: 0.9036 (mtp) cc_final: 0.7798 (ttt) REVERT: A 88 LYS cc_start: 0.8302 (pttp) cc_final: 0.7914 (mttt) REVERT: A 124 ASP cc_start: 0.8560 (m-30) cc_final: 0.8274 (m-30) REVERT: A 147 LYS cc_start: 0.7731 (tptt) cc_final: 0.7115 (tttt) REVERT: A 159 MET cc_start: 0.7974 (mtp) cc_final: 0.7415 (tpt) REVERT: A 164 SER cc_start: 0.7840 (t) cc_final: 0.7358 (p) outliers start: 0 outliers final: 1 residues processed: 84 average time/residue: 1.8569 time to fit residues: 157.8069 Evaluate side-chains 47 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1443 Z= 0.199 Angle : 0.561 3.739 1944 Z= 0.311 Chirality : 0.032 0.122 204 Planarity : 0.003 0.019 257 Dihedral : 4.692 27.805 190 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.23 % Allowed : 24.84 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 1.97 (0.61), residues: 170 helix: 1.85 (0.43), residues: 126 sheet: None (None), residues: 0 loop : -0.22 (0.93), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.010 0.001 TYR A 30 PHE 0.004 0.001 PHE A 171 TRP 0.003 0.001 TRP A 94 HIS 0.006 0.001 HIS A 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9246 (t0) cc_final: 0.8965 (t0) REVERT: A 26 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 64 ARG cc_start: 0.8688 (ttt90) cc_final: 0.8369 (ttp-170) REVERT: A 71 MET cc_start: 0.9054 (mtp) cc_final: 0.8005 (ttt) REVERT: A 88 LYS cc_start: 0.8380 (pttp) cc_final: 0.7903 (mttm) REVERT: A 132 ASP cc_start: 0.7424 (t70) cc_final: 0.6779 (m-30) REVERT: A 147 LYS cc_start: 0.7740 (tptt) cc_final: 0.7188 (tttt) REVERT: A 159 MET cc_start: 0.7891 (mtp) cc_final: 0.7535 (tpt) REVERT: A 164 SER cc_start: 0.7972 (t) cc_final: 0.7409 (p) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 1.5854 time to fit residues: 94.8058 Evaluate side-chains 46 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 14 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 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1443 Z= 0.180 Angle : 0.531 3.552 1944 Z= 0.291 Chirality : 0.031 0.117 204 Planarity : 0.003 0.018 257 Dihedral : 4.633 28.437 190 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.54 % Allowed : 30.72 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 2.79 (0.62), residues: 170 helix: 2.50 (0.43), residues: 126 sheet: None (None), residues: 0 loop : -0.11 (0.96), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 157 TYR 0.014 0.002 TYR A 55 PHE 0.003 0.001 PHE A 171 TRP 0.003 0.001 TRP A 94 HIS 0.003 0.001 HIS A 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9258 (t0) cc_final: 0.8851 (t0) REVERT: A 47 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7719 (m) REVERT: A 64 ARG cc_start: 0.8675 (ttt90) cc_final: 0.8374 (tmm-80) REVERT: A 71 MET cc_start: 0.9033 (mtp) cc_final: 0.8056 (ttt) REVERT: A 88 LYS cc_start: 0.8418 (pttp) cc_final: 0.7901 (mmtt) REVERT: A 147 LYS cc_start: 0.7747 (tptt) cc_final: 0.7142 (mttt) REVERT: A 153 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8108 (t) REVERT: A 159 MET cc_start: 0.7939 (mtp) cc_final: 0.7571 (tpt) REVERT: A 164 SER cc_start: 0.7983 (t) cc_final: 0.7442 (p) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.2477 time to fit residues: 59.5244 Evaluate side-chains 47 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 153 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1443 Z= 0.159 Angle : 0.504 3.294 1944 Z= 0.272 Chirality : 0.030 0.116 204 Planarity : 0.003 0.018 257 Dihedral : 4.572 29.146 190 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.27 % Allowed : 33.99 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.67 (0.63), residues: 170 helix: 3.22 (0.43), residues: 125 sheet: None (None), residues: 0 loop : 0.01 (0.94), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 23 TYR 0.013 0.001 TYR A 30 PHE 0.004 0.001 PHE A 133 TRP 0.004 0.001 TRP A 94 HIS 0.002 0.001 HIS A 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9276 (t0) cc_final: 0.8820 (t0) REVERT: A 47 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7727 (m) REVERT: A 64 ARG cc_start: 0.8654 (ttt90) cc_final: 0.8322 (tmm-80) REVERT: A 71 MET cc_start: 0.9013 (mtp) cc_final: 0.8098 (ttt) REVERT: A 88 LYS cc_start: 0.8541 (pttp) cc_final: 0.7954 (mttt) REVERT: A 132 ASP cc_start: 0.7639 (t0) cc_final: 0.6822 (m-30) REVERT: A 147 LYS cc_start: 0.7725 (tptt) cc_final: 0.7126 (mttt) REVERT: A 159 MET cc_start: 0.7706 (mtp) cc_final: 0.7451 (tpt) REVERT: A 164 SER cc_start: 0.7816 (t) cc_final: 0.7280 (p) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.9215 time to fit residues: 44.9639 Evaluate side-chains 44 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1443 Z= 0.179 Angle : 0.546 3.965 1944 Z= 0.293 Chirality : 0.030 0.113 204 Planarity : 0.003 0.021 257 Dihedral : 4.611 30.049 190 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.54 % Allowed : 32.03 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.58 (0.64), residues: 170 helix: 3.21 (0.44), residues: 127 sheet: None (None), residues: 0 loop : -0.36 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 23 TYR 0.008 0.001 TYR A 13 PHE 0.004 0.001 PHE A 171 TRP 0.002 0.001 TRP A 94 HIS 0.003 0.001 HIS A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.072 Fit side-chains REVERT: A 12 ASN cc_start: 0.9370 (t0) cc_final: 0.8839 (t0) REVERT: A 47 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7746 (m) REVERT: A 64 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8050 (tmm-80) REVERT: A 71 MET cc_start: 0.8882 (mtp) cc_final: 0.8023 (ttt) REVERT: A 88 LYS cc_start: 0.8566 (pttp) cc_final: 0.7942 (mttm) REVERT: A 132 ASP cc_start: 0.7460 (t0) cc_final: 0.6809 (m-30) REVERT: A 147 LYS cc_start: 0.7793 (tptt) cc_final: 0.7355 (tppt) REVERT: A 159 MET cc_start: 0.7759 (mtp) cc_final: 0.7518 (tpt) REVERT: A 164 SER cc_start: 0.7858 (t) cc_final: 0.7343 (p) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.9078 time to fit residues: 41.5195 Evaluate side-chains 45 residues out of total 153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1443 Z= 0.168 Angle : 0.538 4.187 1944 Z= 0.285 Chirality : 0.030 0.114 204 Planarity : 0.003 0.020 257 Dihedral : 4.452 30.008 190 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.27 % Allowed : 35.29 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 3.87 (0.65), residues: 170 helix: 3.49 (0.44), residues: 126 sheet: None (None), residues: 0 loop : -0.40 (0.96), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 23 TYR 0.008 0.001 TYR A 41 PHE 0.003 0.001 PHE A 133 TRP 0.001 0.001 TRP A 94 HIS 0.003 0.001 HIS A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 718.80 seconds wall clock time: 12 minutes 37.74 seconds (757.74 seconds total)