Starting phenix.real_space_refine on Fri Feb 14 04:37:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.map" model { file = "/net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psm_13614/02_2025/7psm_13614.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.096 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6038 2.51 5 N 1602 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 6.47, per 1000 atoms: 0.69 Number of scatterers: 9394 At special positions: 0 Unit cell: (82.467, 77.469, 141.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 8 15.00 Mg 2 11.99 O 1710 8.00 N 1602 7.00 C 6038 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 - 3.00 Amino acid : True - 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 68.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.878A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.598A pdb=" N MET A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.996A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 removed outlier: 3.680A pdb=" N HIS A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 235 Processing helix chain 'A' and resid 235 through 254 removed outlier: 3.828A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 304 removed outlier: 5.370A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 367 removed outlier: 4.052A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 removed outlier: 3.508A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 3.635A pdb=" N TYR A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.962A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.756A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.819A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.593A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 201 removed outlier: 4.022A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 removed outlier: 3.681A pdb=" N HIS B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 235 Processing helix chain 'B' and resid 235 through 254 removed outlier: 3.811A pdb=" N PHE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 304 removed outlier: 5.371A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 313 through 367 removed outlier: 4.052A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 396 removed outlier: 3.502A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Proline residue: B 388 - end of helix removed outlier: 3.620A pdb=" N TYR B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.958A pdb=" N GLY B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.791A pdb=" N GLU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 459 removed outlier: 5.533A pdb=" N ALA A 455 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 441 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER A 490 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 514 through 515 removed outlier: 6.010A pdb=" N VAL A 515 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 596 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 465 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 455 through 459 removed outlier: 5.548A pdb=" N ALA B 455 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 441 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 490 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 514 through 515 removed outlier: 6.019A pdb=" N VAL B 515 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 596 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 465 " --> pdb=" O TYR B 628 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1824 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: 2.73 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1496 1.29 - 1.42: 2402 1.42 - 1.55: 5589 1.55 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 9568 Sorted by residual: bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.309 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C6 ANP B 701 " pdb=" N6 ANP B 701 " ideal model delta sigma weight residual 1.340 1.474 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 9563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 12644 2.86 - 5.72: 220 5.72 - 8.57: 52 8.57 - 11.43: 22 11.43 - 14.29: 4 Bond angle restraints: 12942 Sorted by residual: angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.09 14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.10 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3 LOP A 703 " pdb=" P1 LOP A 703 " pdb=" O4 LOP A 703 " ideal model delta sigma weight residual 120.67 108.32 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O3 LOP B 703 " pdb=" P1 LOP B 703 " pdb=" O4 LOP B 703 " ideal model delta sigma weight residual 120.67 108.34 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ARG B 188 " pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " ideal model delta sigma weight residual 110.88 104.55 6.33 1.57e+00 4.06e-01 1.63e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 5401 26.22 - 52.44: 318 52.44 - 78.66: 61 78.66 - 104.89: 8 104.89 - 131.11: 2 Dihedral angle restraints: 5790 sinusoidal: 2406 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -48.00 131.11 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -47.95 131.06 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C VAL B 128 " pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" CB VAL B 128 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1127 0.054 - 0.109: 300 0.109 - 0.163: 57 0.163 - 0.217: 6 0.217 - 0.272: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CB ILE B 419 " pdb=" CA ILE B 419 " pdb=" CG1 ILE B 419 " pdb=" CG2 ILE B 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 128 " pdb=" CA VAL B 128 " pdb=" CG1 VAL B 128 " pdb=" CG2 VAL B 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1491 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 594 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C MET B 594 " 0.034 2.00e-02 2.50e+03 pdb=" O MET B 594 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 595 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C MET A 594 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 595 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 376 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL A 376 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 376 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 377 " 0.011 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 104 2.64 - 3.21: 8213 3.21 - 3.77: 14658 3.77 - 4.34: 18956 4.34 - 4.90: 32089 Nonbonded interactions: 74020 Sorted by model distance: nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.078 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.093 2.170 nonbonded pdb=" O3G ANP B 701 " pdb="MG MG B 702 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 2.117 2.170 ... (remaining 74015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.710 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.008 0.224 9568 Z= 0.484 Angle : 1.044 14.289 12942 Z= 0.511 Chirality : 0.052 0.272 1494 Planarity : 0.006 0.045 1616 Dihedral : 17.189 131.107 3606 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.20), residues: 1166 helix: -1.52 (0.14), residues: 788 sheet: -3.68 (0.43), residues: 82 loop : -3.03 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 100 HIS 0.005 0.001 HIS B 235 PHE 0.016 0.002 PHE A 179 TYR 0.011 0.002 TYR B 321 ARG 0.002 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.011 Fit side-chains REVERT: A 202 ASP cc_start: 0.7765 (p0) cc_final: 0.7452 (p0) REVERT: A 284 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7570 (ttp80) REVERT: A 350 PHE cc_start: 0.7901 (t80) cc_final: 0.7439 (t80) REVERT: A 383 PHE cc_start: 0.8428 (t80) cc_final: 0.8197 (t80) REVERT: A 628 TYR cc_start: 0.8668 (m-80) cc_final: 0.8279 (m-10) REVERT: B 100 TRP cc_start: 0.7942 (t-100) cc_final: 0.7646 (t60) REVERT: B 202 ASP cc_start: 0.7785 (p0) cc_final: 0.7464 (p0) REVERT: B 284 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7575 (ttp80) REVERT: B 350 PHE cc_start: 0.7915 (t80) cc_final: 0.7448 (t80) REVERT: B 383 PHE cc_start: 0.8424 (t80) cc_final: 0.8182 (t80) REVERT: B 628 TYR cc_start: 0.8673 (m-80) cc_final: 0.8284 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2757 time to fit residues: 66.2903 Evaluate side-chains 135 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 235 HIS A 347 ASN B 127 GLN B 235 HIS B 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098090 restraints weight = 13254.951| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.69 r_work: 0.3098 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9568 Z= 0.197 Angle : 0.545 6.808 12942 Z= 0.284 Chirality : 0.039 0.146 1494 Planarity : 0.004 0.032 1616 Dihedral : 12.934 156.376 1408 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.90 % Allowed : 15.37 % Favored : 82.73 % 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: -0.86 (0.23), residues: 1166 helix: 0.51 (0.18), residues: 790 sheet: -2.55 (0.60), residues: 48 loop : -2.90 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 463 HIS 0.003 0.001 HIS B 197 PHE 0.013 0.001 PHE B 195 TYR 0.007 0.001 TYR B 316 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.040 Fit side-chains REVERT: A 199 MET cc_start: 0.8728 (tpp) cc_final: 0.8376 (mpp) REVERT: A 284 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7712 (ttp80) REVERT: A 350 PHE cc_start: 0.8112 (t80) cc_final: 0.7553 (t80) REVERT: A 383 PHE cc_start: 0.8548 (t80) cc_final: 0.8314 (t80) REVERT: A 572 MET cc_start: 0.8848 (mmm) cc_final: 0.8505 (mmm) REVERT: A 616 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7961 (ttp80) REVERT: A 628 TYR cc_start: 0.8853 (m-80) cc_final: 0.8544 (m-10) REVERT: B 199 MET cc_start: 0.8723 (tpp) cc_final: 0.8364 (mpp) REVERT: B 284 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7770 (ttp80) REVERT: B 350 PHE cc_start: 0.8116 (t80) cc_final: 0.7542 (t80) REVERT: B 359 TYR cc_start: 0.8595 (t80) cc_final: 0.8366 (t80) REVERT: B 383 PHE cc_start: 0.8550 (t80) cc_final: 0.8307 (t80) REVERT: B 396 TYR cc_start: 0.7517 (m-80) cc_final: 0.7230 (m-80) REVERT: B 616 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7916 (ttp80) REVERT: B 628 TYR cc_start: 0.8880 (m-80) cc_final: 0.8574 (m-10) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.2414 time to fit residues: 54.8307 Evaluate side-chains 159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 538 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100600 restraints weight = 13350.965| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.64 r_work: 0.3131 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9568 Z= 0.176 Angle : 0.504 6.679 12942 Z= 0.264 Chirality : 0.039 0.146 1494 Planarity : 0.003 0.033 1616 Dihedral : 10.993 159.730 1408 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.50 % Allowed : 19.16 % Favored : 79.34 % 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: 0.16 (0.25), residues: 1166 helix: 1.43 (0.18), residues: 784 sheet: -2.37 (0.61), residues: 48 loop : -2.81 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 463 HIS 0.003 0.001 HIS A 235 PHE 0.027 0.001 PHE A 234 TYR 0.012 0.001 TYR A 269 ARG 0.003 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.036 Fit side-chains REVERT: A 199 MET cc_start: 0.8682 (tpp) cc_final: 0.8413 (mpp) REVERT: A 284 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7725 (ttp80) REVERT: A 326 MET cc_start: 0.8018 (mmt) cc_final: 0.7727 (mmt) REVERT: A 350 PHE cc_start: 0.8118 (t80) cc_final: 0.7616 (t80) REVERT: A 572 MET cc_start: 0.8764 (mmm) cc_final: 0.8324 (mmm) REVERT: A 616 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7961 (ttp80) REVERT: A 628 TYR cc_start: 0.8848 (m-80) cc_final: 0.8559 (m-10) REVERT: B 199 MET cc_start: 0.8650 (tpp) cc_final: 0.8409 (mpp) REVERT: B 232 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7453 (mmm) REVERT: B 284 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7718 (ttp80) REVERT: B 326 MET cc_start: 0.8021 (mmt) cc_final: 0.7731 (mmt) REVERT: B 350 PHE cc_start: 0.8116 (t80) cc_final: 0.7604 (t80) REVERT: B 359 TYR cc_start: 0.8550 (t80) cc_final: 0.8271 (t80) REVERT: B 572 MET cc_start: 0.8821 (mmm) cc_final: 0.8523 (mmm) REVERT: B 616 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7912 (ttp80) REVERT: B 628 TYR cc_start: 0.8882 (m-80) cc_final: 0.8587 (m-10) outliers start: 15 outliers final: 12 residues processed: 156 average time/residue: 0.2615 time to fit residues: 56.0619 Evaluate side-chains 147 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099222 restraints weight = 13389.048| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.67 r_work: 0.3128 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9568 Z= 0.180 Angle : 0.494 6.591 12942 Z= 0.261 Chirality : 0.039 0.146 1494 Planarity : 0.003 0.032 1616 Dihedral : 10.587 160.372 1408 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.50 % Allowed : 20.26 % Favored : 77.25 % 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: 0.67 (0.25), residues: 1166 helix: 1.87 (0.19), residues: 780 sheet: -2.39 (0.62), residues: 48 loop : -2.68 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 463 HIS 0.010 0.001 HIS A 235 PHE 0.017 0.001 PHE B 234 TYR 0.011 0.001 TYR B 269 ARG 0.003 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.137 Fit side-chains REVERT: A 199 MET cc_start: 0.8609 (tpp) cc_final: 0.8342 (mpp) REVERT: A 235 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6514 (m170) REVERT: A 284 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7659 (ttp80) REVERT: A 347 ASN cc_start: 0.8402 (t0) cc_final: 0.8186 (t0) REVERT: A 350 PHE cc_start: 0.8046 (t80) cc_final: 0.7521 (t80) REVERT: A 396 TYR cc_start: 0.7735 (m-80) cc_final: 0.6676 (m-80) REVERT: A 445 TYR cc_start: 0.8340 (m-80) cc_final: 0.8105 (m-80) REVERT: A 572 MET cc_start: 0.8627 (mmm) cc_final: 0.8235 (tpt) REVERT: A 616 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7960 (ttp80) REVERT: A 628 TYR cc_start: 0.8816 (m-80) cc_final: 0.8499 (m-10) REVERT: B 199 MET cc_start: 0.8562 (tpp) cc_final: 0.8294 (mpp) REVERT: B 232 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: B 235 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6503 (m170) REVERT: B 284 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7655 (ttp80) REVERT: B 347 ASN cc_start: 0.8408 (t0) cc_final: 0.8188 (t0) REVERT: B 350 PHE cc_start: 0.8053 (t80) cc_final: 0.7525 (t80) REVERT: B 359 TYR cc_start: 0.8513 (t80) cc_final: 0.8264 (t80) REVERT: B 392 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7596 (tp) REVERT: B 396 TYR cc_start: 0.7681 (m-80) cc_final: 0.6641 (m-80) REVERT: B 445 TYR cc_start: 0.8361 (m-80) cc_final: 0.8087 (m-80) REVERT: B 628 TYR cc_start: 0.8837 (m-80) cc_final: 0.8572 (m-10) outliers start: 25 outliers final: 15 residues processed: 172 average time/residue: 0.2417 time to fit residues: 56.6670 Evaluate side-chains 154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.0030 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101154 restraints weight = 13252.157| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.67 r_work: 0.3157 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9568 Z= 0.147 Angle : 0.501 10.207 12942 Z= 0.259 Chirality : 0.038 0.142 1494 Planarity : 0.003 0.031 1616 Dihedral : 10.031 160.772 1408 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 21.06 % Favored : 76.55 % 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: 1.09 (0.26), residues: 1166 helix: 2.16 (0.19), residues: 784 sheet: -2.29 (0.62), residues: 48 loop : -2.49 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 100 HIS 0.008 0.001 HIS A 235 PHE 0.020 0.001 PHE B 234 TYR 0.011 0.001 TYR A 269 ARG 0.006 0.000 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.103 Fit side-chains REVERT: A 235 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6559 (m170) REVERT: A 284 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7640 (ttp80) REVERT: A 347 ASN cc_start: 0.8394 (t0) cc_final: 0.8108 (t0) REVERT: A 350 PHE cc_start: 0.8042 (t80) cc_final: 0.7518 (t80) REVERT: A 396 TYR cc_start: 0.7718 (m-80) cc_final: 0.6769 (m-80) REVERT: A 445 TYR cc_start: 0.8301 (m-80) cc_final: 0.8014 (m-80) REVERT: A 572 MET cc_start: 0.8599 (mmm) cc_final: 0.8320 (mmm) REVERT: A 616 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7970 (ttp80) REVERT: A 628 TYR cc_start: 0.8806 (m-80) cc_final: 0.8495 (m-10) REVERT: B 232 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7430 (mmm) REVERT: B 284 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7632 (ttp80) REVERT: B 347 ASN cc_start: 0.8413 (t0) cc_final: 0.8125 (t0) REVERT: B 350 PHE cc_start: 0.8045 (t80) cc_final: 0.7475 (t80) REVERT: B 359 TYR cc_start: 0.8486 (t80) cc_final: 0.8211 (t80) REVERT: B 445 TYR cc_start: 0.8332 (m-80) cc_final: 0.8081 (m-80) REVERT: B 572 MET cc_start: 0.8765 (mmt) cc_final: 0.8490 (mmt) REVERT: B 628 TYR cc_start: 0.8838 (m-80) cc_final: 0.8571 (m-10) outliers start: 24 outliers final: 14 residues processed: 164 average time/residue: 0.2450 time to fit residues: 55.0674 Evaluate side-chains 152 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100249 restraints weight = 13319.714| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.67 r_work: 0.3145 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9568 Z= 0.171 Angle : 0.507 9.648 12942 Z= 0.262 Chirality : 0.039 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.710 158.400 1408 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.69 % Allowed : 20.96 % Favored : 76.35 % 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: 1.23 (0.25), residues: 1166 helix: 2.28 (0.19), residues: 780 sheet: -2.02 (0.62), residues: 48 loop : -2.45 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 100 HIS 0.009 0.001 HIS B 235 PHE 0.020 0.001 PHE B 234 TYR 0.011 0.001 TYR B 269 ARG 0.006 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.012 Fit side-chains REVERT: A 235 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6590 (m170) REVERT: A 284 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7653 (ttp80) REVERT: A 347 ASN cc_start: 0.8466 (t0) cc_final: 0.8100 (t0) REVERT: A 350 PHE cc_start: 0.8028 (t80) cc_final: 0.7496 (t80) REVERT: A 396 TYR cc_start: 0.7780 (m-80) cc_final: 0.6969 (m-80) REVERT: A 445 TYR cc_start: 0.8342 (m-80) cc_final: 0.8097 (m-80) REVERT: A 572 MET cc_start: 0.8583 (mmm) cc_final: 0.8259 (mmm) REVERT: A 616 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7956 (ttp80) REVERT: A 628 TYR cc_start: 0.8799 (m-80) cc_final: 0.8498 (m-10) REVERT: A 659 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7946 (mm) REVERT: B 232 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7498 (mmm) REVERT: B 235 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6626 (m170) REVERT: B 284 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7650 (ttp80) REVERT: B 347 ASN cc_start: 0.8490 (t0) cc_final: 0.8115 (t0) REVERT: B 350 PHE cc_start: 0.8054 (t80) cc_final: 0.7468 (t80) REVERT: B 359 TYR cc_start: 0.8507 (t80) cc_final: 0.8257 (t80) REVERT: B 396 TYR cc_start: 0.7706 (m-80) cc_final: 0.6882 (m-80) REVERT: B 572 MET cc_start: 0.8755 (mmt) cc_final: 0.8375 (mmt) REVERT: B 628 TYR cc_start: 0.8829 (m-80) cc_final: 0.8512 (m-10) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.2393 time to fit residues: 53.7779 Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100268 restraints weight = 13306.594| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.67 r_work: 0.3147 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9568 Z= 0.169 Angle : 0.503 9.100 12942 Z= 0.260 Chirality : 0.039 0.145 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.416 157.260 1408 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.79 % Allowed : 21.26 % Favored : 75.95 % 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: 1.34 (0.25), residues: 1166 helix: 2.35 (0.19), residues: 780 sheet: -1.85 (0.63), residues: 48 loop : -2.39 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.021 0.001 PHE B 234 TYR 0.010 0.001 TYR A 269 ARG 0.004 0.000 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.986 Fit side-chains REVERT: A 199 MET cc_start: 0.8564 (tpp) cc_final: 0.8129 (mpp) REVERT: A 235 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6707 (m170) REVERT: A 284 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7650 (ttp80) REVERT: A 347 ASN cc_start: 0.8527 (t160) cc_final: 0.8141 (t0) REVERT: A 350 PHE cc_start: 0.7999 (t80) cc_final: 0.7459 (t80) REVERT: A 572 MET cc_start: 0.8535 (mmm) cc_final: 0.8232 (mmm) REVERT: A 616 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7968 (ttp80) REVERT: A 628 TYR cc_start: 0.8807 (m-80) cc_final: 0.8506 (m-10) REVERT: A 659 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (mm) REVERT: B 199 MET cc_start: 0.8543 (tpp) cc_final: 0.8111 (mpp) REVERT: B 232 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7510 (mmm) REVERT: B 235 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6625 (m170) REVERT: B 284 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 347 ASN cc_start: 0.8524 (t160) cc_final: 0.8135 (t0) REVERT: B 350 PHE cc_start: 0.8039 (t80) cc_final: 0.7449 (t80) REVERT: B 359 TYR cc_start: 0.8500 (t80) cc_final: 0.8245 (t80) REVERT: B 572 MET cc_start: 0.8732 (mmt) cc_final: 0.8364 (mmt) REVERT: B 628 TYR cc_start: 0.8831 (m-80) cc_final: 0.8511 (m-10) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.2401 time to fit residues: 52.0867 Evaluate side-chains 159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100279 restraints weight = 13568.821| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.70 r_work: 0.3146 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9568 Z= 0.174 Angle : 0.513 8.949 12942 Z= 0.267 Chirality : 0.040 0.144 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.302 156.585 1408 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.79 % Allowed : 21.76 % Favored : 75.45 % 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: 1.42 (0.25), residues: 1166 helix: 2.39 (0.19), residues: 780 sheet: -1.78 (0.63), residues: 48 loop : -2.31 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.019 0.001 PHE B 234 TYR 0.011 0.001 TYR B 269 ARG 0.007 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.015 Fit side-chains REVERT: A 199 MET cc_start: 0.8590 (tpp) cc_final: 0.8174 (mpp) REVERT: A 235 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6688 (m170) REVERT: A 284 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7657 (ttp80) REVERT: A 347 ASN cc_start: 0.8542 (t160) cc_final: 0.8083 (t0) REVERT: A 350 PHE cc_start: 0.8017 (t80) cc_final: 0.7453 (t80) REVERT: A 572 MET cc_start: 0.8540 (mmm) cc_final: 0.8213 (mmm) REVERT: A 616 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7967 (ttp80) REVERT: A 628 TYR cc_start: 0.8808 (m-80) cc_final: 0.8503 (m-10) REVERT: A 659 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (mm) REVERT: B 199 MET cc_start: 0.8577 (tpp) cc_final: 0.8164 (mpp) REVERT: B 232 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: B 235 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6573 (m170) REVERT: B 284 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 347 ASN cc_start: 0.8546 (t160) cc_final: 0.8082 (t0) REVERT: B 350 PHE cc_start: 0.8040 (t80) cc_final: 0.7509 (t80) REVERT: B 359 TYR cc_start: 0.8463 (t80) cc_final: 0.8189 (t80) REVERT: B 396 TYR cc_start: 0.7596 (m-80) cc_final: 0.6877 (m-80) REVERT: B 572 MET cc_start: 0.8764 (mmt) cc_final: 0.8399 (mmt) REVERT: B 628 TYR cc_start: 0.8830 (m-80) cc_final: 0.8564 (m-10) outliers start: 28 outliers final: 23 residues processed: 157 average time/residue: 0.2489 time to fit residues: 53.2029 Evaluate side-chains 159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 11 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102437 restraints weight = 13233.958| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.70 r_work: 0.3175 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9568 Z= 0.142 Angle : 0.497 8.640 12942 Z= 0.259 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.038 154.119 1408 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.30 % Allowed : 22.46 % Favored : 75.25 % 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: 1.44 (0.25), residues: 1166 helix: 2.43 (0.19), residues: 786 sheet: -1.53 (0.63), residues: 48 loop : -2.51 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.018 0.001 PHE B 234 TYR 0.010 0.001 TYR B 269 ARG 0.007 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.081 Fit side-chains REVERT: A 199 MET cc_start: 0.8611 (tpp) cc_final: 0.8237 (mpp) REVERT: A 235 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6585 (m170) REVERT: A 284 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7647 (ttp80) REVERT: A 347 ASN cc_start: 0.8541 (t160) cc_final: 0.8131 (t0) REVERT: A 350 PHE cc_start: 0.7975 (t80) cc_final: 0.7454 (t80) REVERT: A 396 TYR cc_start: 0.7772 (m-80) cc_final: 0.6970 (m-80) REVERT: A 572 MET cc_start: 0.8534 (mmm) cc_final: 0.8202 (mmm) REVERT: A 616 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7963 (ttp80) REVERT: A 628 TYR cc_start: 0.8802 (m-80) cc_final: 0.8553 (m-10) REVERT: A 659 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8031 (mm) REVERT: B 199 MET cc_start: 0.8580 (tpp) cc_final: 0.8207 (mpp) REVERT: B 232 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7441 (mmm) REVERT: B 235 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6520 (m170) REVERT: B 284 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7641 (ttp80) REVERT: B 347 ASN cc_start: 0.8587 (t160) cc_final: 0.8119 (t0) REVERT: B 350 PHE cc_start: 0.7981 (t80) cc_final: 0.7453 (t80) REVERT: B 396 TYR cc_start: 0.7605 (m-80) cc_final: 0.6850 (m-80) REVERT: B 572 MET cc_start: 0.8779 (mmt) cc_final: 0.8376 (mmt) REVERT: B 628 TYR cc_start: 0.8815 (m-80) cc_final: 0.8543 (m-10) outliers start: 23 outliers final: 18 residues processed: 162 average time/residue: 0.2351 time to fit residues: 52.4172 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100212 restraints weight = 13533.482| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.69 r_work: 0.3142 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9568 Z= 0.192 Angle : 0.533 8.905 12942 Z= 0.275 Chirality : 0.040 0.145 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.104 153.859 1408 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 22.85 % Favored : 74.75 % 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: 1.58 (0.26), residues: 1166 helix: 2.47 (0.19), residues: 780 sheet: -1.41 (0.64), residues: 48 loop : -2.18 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.015 0.001 PHE B 234 TYR 0.011 0.001 TYR A 269 ARG 0.007 0.000 ARG A 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.046 Fit side-chains REVERT: A 199 MET cc_start: 0.8609 (tpp) cc_final: 0.8214 (mpp) REVERT: A 235 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6661 (m170) REVERT: A 284 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7658 (ttp80) REVERT: A 347 ASN cc_start: 0.8610 (t160) cc_final: 0.8137 (t0) REVERT: A 350 PHE cc_start: 0.7995 (t80) cc_final: 0.7440 (t80) REVERT: A 396 TYR cc_start: 0.7647 (m-80) cc_final: 0.6874 (m-80) REVERT: A 572 MET cc_start: 0.8496 (mmm) cc_final: 0.8177 (mmm) REVERT: A 616 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7972 (ttp80) REVERT: A 628 TYR cc_start: 0.8796 (m-80) cc_final: 0.8483 (m-10) REVERT: A 659 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8000 (mm) REVERT: B 199 MET cc_start: 0.8604 (tpp) cc_final: 0.8204 (mpp) REVERT: B 232 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7479 (mmm) REVERT: B 235 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6557 (m170) REVERT: B 284 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7639 (ttp80) REVERT: B 347 ASN cc_start: 0.8613 (t160) cc_final: 0.8146 (t0) REVERT: B 350 PHE cc_start: 0.8008 (t80) cc_final: 0.7416 (t80) REVERT: B 396 TYR cc_start: 0.7599 (m-80) cc_final: 0.6881 (m-80) REVERT: B 572 MET cc_start: 0.8752 (mmt) cc_final: 0.8323 (mmt) REVERT: B 628 TYR cc_start: 0.8819 (m-80) cc_final: 0.8552 (m-10) outliers start: 24 outliers final: 20 residues processed: 154 average time/residue: 0.2389 time to fit residues: 50.6893 Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100236 restraints weight = 13373.562| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.68 r_work: 0.3145 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9568 Z= 0.179 Angle : 0.530 9.016 12942 Z= 0.274 Chirality : 0.040 0.143 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.060 153.999 1408 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.50 % Allowed : 23.05 % Favored : 74.45 % 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: 1.60 (0.25), residues: 1166 helix: 2.48 (0.19), residues: 780 sheet: -1.30 (0.66), residues: 48 loop : -2.15 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 463 HIS 0.008 0.001 HIS B 235 PHE 0.015 0.001 PHE A 234 TYR 0.011 0.001 TYR B 269 ARG 0.007 0.000 ARG A 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3615.09 seconds wall clock time: 65 minutes 17.73 seconds (3917.73 seconds total)