Starting phenix.real_space_refine on Mon Sep 23 18:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/09_2024/7zyz_15029.cif" } resolution = 2.47 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 19 5.16 5 C 2740 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4349 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4301 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 48 Unusual residues: {' MN': 1, 'OAA': 1} Classifications: {'undetermined': 2, 'water': 38} Link IDs: {None: 39} Time building chain proxies: 3.63, per 1000 atoms: 0.83 Number of scatterers: 4349 At special positions: 0 Unit cell: (73.14, 77.38, 80.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 19 16.00 O 858 8.00 N 731 7.00 C 2740 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: 1.44 Conformation dependent library (CDL) restraints added in 525.6 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 60.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 522 removed outlier: 8.050A pdb=" N ALA A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ASP A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.713A pdb=" N GLY A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.801A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 631 Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.567A pdb=" N TYR A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.518A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.907A pdb=" N VAL A 820 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 836 Processing helix chain 'A' and resid 845 through 860 removed outlier: 4.077A pdb=" N GLN A 851 " --> pdb=" O ASP A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.714A pdb=" N VAL A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 945 through 958 removed outlier: 3.908A pdb=" N LYS A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 986 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.773A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 601 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 637 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET A 603 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A 733 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 567 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: 1.20 Time building geometry restraints manager: 1.42 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: 1426 1.34 - 1.46: 731 1.46 - 1.57: 2210 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4404 Sorted by residual: bond pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 1.329 1.427 -0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sigma weight residual 1.214 1.307 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 OAA A1202 " pdb=" O2 OAA A1202 " ideal model delta sigma weight residual 1.242 1.311 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 OAA A1202 " pdb=" O4 OAA A1202 " ideal model delta sigma weight residual 1.241 1.308 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 4399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.66: 5958 7.66 - 15.32: 2 15.32 - 22.98: 0 22.98 - 30.64: 0 30.64 - 38.30: 1 Bond angle restraints: 5961 Sorted by residual: angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 84.70 38.30 1.60e+00 3.91e-01 5.73e+02 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA LYS A 501 " pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.28e+00 angle pdb=" N ALA A 837 " pdb=" CA ALA A 837 " pdb=" C ALA A 837 " ideal model delta sigma weight residual 112.72 109.10 3.62 1.28e+00 6.10e-01 7.99e+00 ... (remaining 5956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2517 32.62 - 65.24: 118 65.24 - 97.86: 13 97.86 - 130.48: 0 130.48 - 163.10: 1 Dihedral angle restraints: 2649 sinusoidal: 1080 harmonic: 1569 Sorted by residual: dihedral pdb=" C1 OAA A1202 " pdb=" C2 OAA A1202 " pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sinusoidal sigma weight residual -102.23 60.87 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA ASN A 609 " pdb=" C ASN A 609 " pdb=" N ALA A 610 " pdb=" CA ALA A 610 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 648 " pdb=" C MET A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 322 0.031 - 0.062: 203 0.062 - 0.093: 90 0.093 - 0.124: 28 0.124 - 0.155: 7 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA LYS A 500 " pdb=" N LYS A 500 " pdb=" C LYS A 500 " pdb=" CB LYS A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA THR A 994 " pdb=" N THR A 994 " pdb=" C THR A 994 " pdb=" CB THR A 994 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 647 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.143 2.00e-02 2.50e+03 2.27e-01 5.14e+02 pdb=" C VAL A 702 " -0.390 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.156 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 501 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LYS A 501 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 501 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 502 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 867 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 868 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 868 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 868 " -0.019 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 60 2.56 - 3.14: 3618 3.14 - 3.73: 7536 3.73 - 4.31: 10651 4.31 - 4.90: 16713 Nonbonded interactions: 38578 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1201 " model vdw 1.973 2.320 nonbonded pdb="MN MN A1201 " pdb=" O HOH A1320 " model vdw 2.002 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1201 " model vdw 2.030 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1201 " model vdw 2.143 2.320 nonbonded pdb=" O HIS A 823 " pdb=" ND1 HIS A 823 " model vdw 2.151 3.120 ... (remaining 38573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 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 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: 1.480 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.098 4404 Z= 0.481 Angle : 0.871 38.295 5961 Z= 0.491 Chirality : 0.047 0.155 650 Planarity : 0.009 0.227 780 Dihedral : 18.664 163.102 1645 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.45 % Allowed : 18.95 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.23 (0.36), residues: 536 helix: -0.09 (0.30), residues: 294 sheet: -0.53 (0.73), residues: 43 loop : 0.14 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 799 HIS 0.003 0.001 HIS A 844 PHE 0.018 0.002 PHE A 879 TYR 0.013 0.002 TYR A 715 ARG 0.003 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.511 Fit side-chains REVERT: A 460 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5987 (mmt-90) outliers start: 25 outliers final: 24 residues processed: 60 average time/residue: 1.0991 time to fit residues: 68.9816 Evaluate side-chains 58 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 33 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4404 Z= 0.221 Angle : 0.539 6.625 5961 Z= 0.293 Chirality : 0.042 0.134 650 Planarity : 0.004 0.036 780 Dihedral : 10.877 160.969 644 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.01 % Allowed : 18.30 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.58 (0.37), residues: 536 helix: 0.54 (0.30), residues: 293 sheet: -0.46 (0.71), residues: 43 loop : 0.65 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 PHE 0.015 0.001 PHE A 879 TYR 0.010 0.001 TYR A 853 ARG 0.002 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 34 time to evaluate : 0.531 Fit side-chains outliers start: 23 outliers final: 6 residues processed: 53 average time/residue: 1.1013 time to fit residues: 61.3217 Evaluate side-chains 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4404 Z= 0.249 Angle : 0.569 10.085 5961 Z= 0.300 Chirality : 0.043 0.141 650 Planarity : 0.004 0.035 780 Dihedral : 9.438 158.680 606 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.83 % Allowed : 18.52 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.72 (0.37), residues: 536 helix: 0.73 (0.31), residues: 293 sheet: -0.65 (0.68), residues: 43 loop : 0.63 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.015 0.002 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.522 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 43 average time/residue: 0.8383 time to fit residues: 38.3875 Evaluate side-chains 40 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4404 Z= 0.269 Angle : 0.559 8.392 5961 Z= 0.299 Chirality : 0.043 0.138 650 Planarity : 0.004 0.034 780 Dihedral : 9.334 158.068 604 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.92 % Allowed : 17.86 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.74 (0.37), residues: 536 helix: 0.79 (0.31), residues: 293 sheet: -0.75 (0.70), residues: 43 loop : 0.59 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 PHE 0.016 0.002 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 34 time to evaluate : 0.571 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 49 average time/residue: 1.0175 time to fit residues: 52.4439 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A 955 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4404 Z= 0.176 Angle : 0.516 9.176 5961 Z= 0.275 Chirality : 0.041 0.132 650 Planarity : 0.004 0.033 780 Dihedral : 9.104 155.418 604 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.70 % Allowed : 18.52 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.82 (0.37), residues: 536 helix: 0.90 (0.32), residues: 295 sheet: -0.66 (0.72), residues: 43 loop : 0.54 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.014 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 33 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 691 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6942 (tp30) outliers start: 17 outliers final: 5 residues processed: 49 average time/residue: 1.0690 time to fit residues: 55.0338 Evaluate side-chains 38 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 955 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4404 Z= 0.166 Angle : 0.523 9.958 5961 Z= 0.273 Chirality : 0.040 0.132 650 Planarity : 0.004 0.032 780 Dihedral : 8.983 154.718 603 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.27 % Allowed : 19.39 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.92 (0.37), residues: 536 helix: 0.98 (0.32), residues: 295 sheet: -0.62 (0.73), residues: 43 loop : 0.58 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.013 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8151 (tp) REVERT: A 691 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6692 (tp30) outliers start: 15 outliers final: 7 residues processed: 48 average time/residue: 1.2005 time to fit residues: 60.7773 Evaluate side-chains 41 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4404 Z= 0.210 Angle : 0.557 11.277 5961 Z= 0.291 Chirality : 0.041 0.133 650 Planarity : 0.004 0.032 780 Dihedral : 9.050 154.595 603 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.05 % Allowed : 19.61 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.90 (0.37), residues: 536 helix: 0.94 (0.32), residues: 294 sheet: -0.62 (0.73), residues: 43 loop : 0.61 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 PHE 0.014 0.001 PHE A 879 TYR 0.011 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 691 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6721 (tp30) outliers start: 14 outliers final: 7 residues processed: 45 average time/residue: 1.1334 time to fit residues: 53.6350 Evaluate side-chains 41 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4404 Z= 0.239 Angle : 0.577 11.825 5961 Z= 0.301 Chirality : 0.042 0.145 650 Planarity : 0.004 0.033 780 Dihedral : 9.115 155.222 603 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 19.83 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.93 (0.38), residues: 536 helix: 0.94 (0.32), residues: 293 sheet: -0.67 (0.74), residues: 43 loop : 0.70 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 PHE 0.014 0.001 PHE A 879 TYR 0.011 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 691 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6727 (tp30) outliers start: 15 outliers final: 10 residues processed: 45 average time/residue: 1.0418 time to fit residues: 49.5186 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4404 Z= 0.244 Angle : 0.584 10.872 5961 Z= 0.307 Chirality : 0.043 0.175 650 Planarity : 0.004 0.033 780 Dihedral : 9.128 155.362 603 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.05 % Allowed : 19.61 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.93 (0.38), residues: 536 helix: 0.92 (0.31), residues: 293 sheet: -0.66 (0.73), residues: 43 loop : 0.72 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 PHE 0.014 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 691 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6725 (tp30) outliers start: 14 outliers final: 10 residues processed: 45 average time/residue: 1.0334 time to fit residues: 49.1390 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4404 Z= 0.195 Angle : 0.568 12.579 5961 Z= 0.297 Chirality : 0.041 0.180 650 Planarity : 0.004 0.032 780 Dihedral : 8.966 153.863 603 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.83 % Allowed : 20.26 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.96 (0.38), residues: 536 helix: 0.97 (0.32), residues: 294 sheet: -0.63 (0.74), residues: 43 loop : 0.69 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.013 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 645 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (tp) REVERT: A 691 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6687 (tp30) outliers start: 13 outliers final: 8 residues processed: 44 average time/residue: 1.0146 time to fit residues: 47.1492 Evaluate side-chains 42 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 34 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061507 restraints weight = 12209.102| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.66 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4404 Z= 0.203 Angle : 0.577 12.861 5961 Z= 0.301 Chirality : 0.042 0.194 650 Planarity : 0.004 0.032 780 Dihedral : 8.982 153.719 603 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.61 % Allowed : 20.26 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.94 (0.38), residues: 536 helix: 0.96 (0.32), residues: 294 sheet: -0.63 (0.74), residues: 43 loop : 0.67 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.012 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.004 0.000 ARG A 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.39 seconds wall clock time: 33 minutes 11.63 seconds (1991.63 seconds total)