Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/11_2022/5m5h_4155.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 1086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1086 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.27, per 1000 atoms: 1.17 Number of scatterers: 1086 At special positions: 0 Unit cell: (54.2, 49.864, 54.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 164 8.00 N 157 7.00 C 757 6.00 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: 0.39 Conformation dependent library (CDL) restraints added in 153.7 milliseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 425 through 428 removed outlier: 3.881A pdb=" N ILE A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.714A pdb=" N ILE A 469 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 removed outlier: 3.501A pdb=" N THR A 496 " --> pdb=" O LYS A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.510A pdb=" N ILE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 527 removed outlier: 3.932A pdb=" N VAL A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) 55 hydrogen bonds defined for protein. 165 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: 0.23 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 240 1.34 - 1.46: 290 1.46 - 1.58: 581 1.58 - 1.70: 0 1.70 - 1.82: 15 Bond restraints: 1126 Sorted by residual: bond pdb=" C MET A 498 " pdb=" O MET A 498 " ideal model delta sigma weight residual 1.238 1.222 0.016 9.50e-03 1.11e+04 2.79e+00 bond pdb=" CA VAL A 351 " pdb=" C VAL A 351 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.31e-02 5.83e+03 2.58e+00 bond pdb=" CA TYR A 465 " pdb=" C TYR A 465 " ideal model delta sigma weight residual 1.525 1.547 -0.021 1.40e-02 5.10e+03 2.30e+00 bond pdb=" C PHE A 502 " pdb=" O PHE A 502 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.15e-02 7.56e+03 2.03e+00 bond pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 1.465 1.451 0.014 1.05e-02 9.07e+03 1.75e+00 ... (remaining 1121 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.20: 36 105.20 - 112.45: 521 112.45 - 119.70: 429 119.70 - 126.94: 527 126.94 - 134.19: 24 Bond angle restraints: 1537 Sorted by residual: angle pdb=" C TRP A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 122.26 114.49 7.77 1.59e+00 3.96e-01 2.39e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 113.18 124.74 -11.56 2.37e+00 1.78e-01 2.38e+01 angle pdb=" C CYS A 423 " pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 122.28 117.93 4.35 1.02e+00 9.61e-01 1.82e+01 angle pdb=" CA TYR A 464 " pdb=" CB TYR A 464 " pdb=" CG TYR A 464 " ideal model delta sigma weight residual 113.90 121.19 -7.29 1.80e+00 3.09e-01 1.64e+01 angle pdb=" C PHE A 497 " pdb=" N MET A 498 " pdb=" CA MET A 498 " ideal model delta sigma weight residual 121.62 127.11 -5.49 1.57e+00 4.06e-01 1.22e+01 ... (remaining 1532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.25: 467 8.25 - 16.50: 103 16.50 - 24.75: 40 24.75 - 33.00: 10 33.00 - 41.25: 12 Dihedral angle restraints: 632 sinusoidal: 244 harmonic: 388 Sorted by residual: dihedral pdb=" CA PHE A 424 " pdb=" C PHE A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 141.50 38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA VAL A 351 " pdb=" C VAL A 351 " pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLN A 527 " pdb=" C GLN A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 90 0.047 - 0.094: 53 0.094 - 0.141: 17 0.141 - 0.188: 10 0.188 - 0.235: 4 Chirality restraints: 174 Sorted by residual: chirality pdb=" CG LEU A 446 " pdb=" CB LEU A 446 " pdb=" CD1 LEU A 446 " pdb=" CD2 LEU A 446 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU A 446 " pdb=" N LEU A 446 " pdb=" C LEU A 446 " pdb=" CB LEU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 171 not shown) Planarity restraints: 180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " -0.032 2.00e-02 2.50e+03 2.14e-02 9.15e+00 pdb=" CG TYR A 517 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 467 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 468 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 424 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 425 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.036 5.00e-02 4.00e+02 ... (remaining 177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 107 2.73 - 3.27: 1132 3.27 - 3.81: 1718 3.81 - 4.36: 2184 4.36 - 4.90: 3185 Nonbonded interactions: 8326 Sorted by model distance: nonbonded pdb=" O MET A 498 " pdb=" N ILE A 501 " model vdw 2.186 2.520 nonbonded pdb=" O LEU A 344 " pdb=" ND1 HIS A 348 " model vdw 2.310 2.520 nonbonded pdb=" O PHE A 506 " pdb=" N PHE A 509 " model vdw 2.361 2.520 nonbonded pdb=" O ILE A 364 " pdb=" N GLY A 367 " model vdw 2.381 2.520 nonbonded pdb=" O LEU A 426 " pdb=" N GLN A 429 " model vdw 2.384 2.520 ... (remaining 8321 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 757 2.51 5 N 157 2.21 5 O 164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.330 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: 15.590 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.010 Process input model: 10.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1430 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 : 0.007 0.044 1126 Z= 0.465 Angle : 1.499 11.564 1537 Z= 0.831 Chirality : 0.075 0.235 174 Planarity : 0.011 0.067 180 Dihedral : 12.373 41.255 380 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 39.89 Ramachandran Plot: Outliers : 2.38 % Allowed : 8.73 % Favored : 88.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % Twisted Proline : 11.11 % Twisted General : 0.83 % 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: -5.94 (0.48), residues: 126 helix: -3.97 (0.37), residues: 70 sheet: None (None), residues: 0 loop : -3.84 (0.60), residues: 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0866 time to fit residues: 2.4062 Evaluate side-chains 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1395 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 1126 Z= 0.245 Angle : 0.946 8.180 1537 Z= 0.488 Chirality : 0.053 0.155 174 Planarity : 0.010 0.060 180 Dihedral : 8.638 28.517 138 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -4.20 (0.60), residues: 126 helix: -2.14 (0.47), residues: 75 sheet: None (None), residues: 0 loop : -3.75 (0.74), residues: 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0776 time to fit residues: 1.9481 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1349 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 1126 Z= 0.217 Angle : 0.855 6.513 1537 Z= 0.432 Chirality : 0.052 0.190 174 Planarity : 0.009 0.067 180 Dihedral : 7.658 28.771 138 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 1.59 % Allowed : 7.94 % Favored : 90.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -3.09 (0.67), residues: 126 helix: -1.32 (0.51), residues: 78 sheet: None (None), residues: 0 loop : -3.23 (0.85), residues: 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0795 time to fit residues: 1.8995 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 0.0000 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1291 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1126 Z= 0.192 Angle : 0.824 7.748 1537 Z= 0.406 Chirality : 0.050 0.188 174 Planarity : 0.008 0.051 180 Dihedral : 6.762 23.276 138 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.39 (0.68), residues: 126 helix: -0.59 (0.54), residues: 82 sheet: None (None), residues: 0 loop : -3.52 (0.77), residues: 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.121 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0750 time to fit residues: 1.6289 Evaluate side-chains 13 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 0.0570 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1244 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1126 Z= 0.181 Angle : 0.787 8.253 1537 Z= 0.381 Chirality : 0.048 0.201 174 Planarity : 0.008 0.051 180 Dihedral : 6.107 21.585 138 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.57 (0.71), residues: 126 helix: -0.06 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -2.95 (0.84), residues: 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0779 time to fit residues: 1.5970 Evaluate side-chains 13 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.0040 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1271 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1126 Z= 0.201 Angle : 0.803 7.963 1537 Z= 0.398 Chirality : 0.050 0.196 174 Planarity : 0.007 0.044 180 Dihedral : 6.042 18.577 138 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.34 (0.73), residues: 126 helix: 0.29 (0.57), residues: 82 sheet: None (None), residues: 0 loop : -3.25 (0.80), residues: 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0733 time to fit residues: 1.5198 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1308 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 1126 Z= 0.200 Angle : 0.836 9.121 1537 Z= 0.409 Chirality : 0.052 0.233 174 Planarity : 0.007 0.046 180 Dihedral : 6.004 18.162 138 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.56 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.69 (0.69), residues: 126 helix: 0.12 (0.54), residues: 83 sheet: None (None), residues: 0 loop : -3.70 (0.71), residues: 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0950 time to fit residues: 2.1815 Evaluate side-chains 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.0370 chunk 9 optimal weight: 20.0000 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1278 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.204 Angle : 0.824 10.019 1537 Z= 0.406 Chirality : 0.053 0.205 174 Planarity : 0.007 0.048 180 Dihedral : 5.961 19.392 138 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.56 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.55 (0.70), residues: 126 helix: 0.21 (0.56), residues: 83 sheet: None (None), residues: 0 loop : -3.63 (0.71), residues: 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0738 time to fit residues: 1.6370 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.0040 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1283 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 1126 Z= 0.214 Angle : 0.855 8.564 1537 Z= 0.421 Chirality : 0.052 0.152 174 Planarity : 0.007 0.049 180 Dihedral : 6.082 18.430 138 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.58 (0.71), residues: 126 helix: 0.20 (0.56), residues: 83 sheet: None (None), residues: 0 loop : -3.65 (0.73), residues: 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0718 time to fit residues: 1.5649 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1240 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.201 Angle : 0.825 8.454 1537 Z= 0.408 Chirality : 0.051 0.152 174 Planarity : 0.007 0.048 180 Dihedral : 5.975 19.959 138 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.35 (0.73), residues: 126 helix: 0.33 (0.57), residues: 83 sheet: None (None), residues: 0 loop : -3.45 (0.76), residues: 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0724 time to fit residues: 1.4865 Evaluate side-chains 14 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.202489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.196323 restraints weight = 4548.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.197810 restraints weight = 3256.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.198986 restraints weight = 2368.114| |-----------------------------------------------------------------------------| r_work (final): 0.4885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1364 moved from start: 0.8618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 1126 Z= 0.228 Angle : 0.857 8.163 1537 Z= 0.432 Chirality : 0.053 0.167 174 Planarity : 0.007 0.049 180 Dihedral : 6.281 18.320 138 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.85 (0.68), residues: 126 helix: -0.13 (0.54), residues: 83 sheet: None (None), residues: 0 loop : -3.47 (0.76), residues: 43 =============================================================================== Job complete usr+sys time: 838.07 seconds wall clock time: 15 minutes 31.01 seconds (931.01 seconds total)