Starting phenix.real_space_refine on Tue Feb 11 06:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_15029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_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/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_15029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_15029.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_15029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyz_15029/02_2025/7zyz_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-5592/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: 3.19, per 1000 atoms: 0.73 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: 1.24 Conformation dependent library (CDL) restraints added in 503.5 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: 0.47 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: 1.27 Time building geometry restraints manager: 1.35 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: 4.490 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 12.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.502 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: 1.2954 time to fit residues: 81.0685 Evaluate side-chains 58 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060329 restraints weight = 12042.572| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.59 r_work: 0.3050 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.535 Fit side-chains REVERT: A 852 MET cc_start: 0.8860 (tpt) cc_final: 0.8526 (tpp) outliers start: 23 outliers final: 6 residues processed: 53 average time/residue: 1.1486 time to fit residues: 63.6360 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.069342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060748 restraints weight = 12055.587| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.61 r_work: 0.3063 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4404 Z= 0.201 Angle : 0.536 10.203 5961 Z= 0.285 Chirality : 0.042 0.134 650 Planarity : 0.004 0.033 780 Dihedral : 9.335 158.493 606 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.61 % Allowed : 19.17 % 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: 0.76 (0.37), residues: 536 helix: 0.78 (0.31), residues: 294 sheet: -0.63 (0.69), residues: 43 loop : 0.62 (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 0.015 0.001 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 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.542 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 42 average time/residue: 0.9453 time to fit residues: 42.0716 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 968 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.068887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060217 restraints weight = 12192.687| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.64 r_work: 0.3049 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1478 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= 0.243 Angle : 0.543 8.103 5961 Z= 0.290 Chirality : 0.043 0.136 650 Planarity : 0.004 0.034 780 Dihedral : 9.244 157.281 603 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % 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: 0.75 (0.37), residues: 536 helix: 0.82 (0.31), residues: 294 sheet: -0.77 (0.70), residues: 43 loop : 0.57 (0.47), 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 0.015 0.001 PHE A 879 TYR 0.011 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 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.557 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 47 average time/residue: 1.0986 time to fit residues: 54.2442 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061037 restraints weight = 12400.642| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.67 r_work: 0.3072 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4404 Z= 0.181 Angle : 0.512 9.029 5961 Z= 0.273 Chirality : 0.041 0.132 650 Planarity : 0.004 0.033 780 Dihedral : 9.076 155.371 603 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.05 % Allowed : 18.95 % Favored : 78.00 % 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: -0.70 (0.72), residues: 43 loop : 0.55 (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 0.011 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 47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.526 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 46 average time/residue: 1.0089 time to fit residues: 48.8776 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060703 restraints weight = 12164.251| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.65 r_work: 0.3063 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4404 Z= 0.223 Angle : 0.553 9.325 5961 Z= 0.290 Chirality : 0.042 0.142 650 Planarity : 0.004 0.033 780 Dihedral : 9.122 155.495 603 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.05 % Allowed : 19.39 % Favored : 77.56 % 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: 0.86 (0.37), residues: 536 helix: 0.90 (0.31), residues: 294 sheet: -0.67 (0.73), residues: 43 loop : 0.62 (0.47), 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 0.005 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 47 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 1.0957 time to fit residues: 51.8271 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 867 THR Chi-restraints excluded: chain A residue 915 VAL 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 3 optimal weight: 0.0470 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.069542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060849 restraints weight = 12271.045| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.66 r_work: 0.3068 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4404 Z= 0.219 Angle : 0.556 10.982 5961 Z= 0.290 Chirality : 0.042 0.152 650 Planarity : 0.004 0.033 780 Dihedral : 9.097 155.024 603 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.49 % Allowed : 19.39 % 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: 0.84 (0.37), residues: 536 helix: 0.92 (0.31), residues: 295 sheet: -0.64 (0.74), residues: 43 loop : 0.53 (0.46), residues: 198 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 50 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.514 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 49 average time/residue: 1.0342 time to fit residues: 53.3326 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 705 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.070086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061596 restraints weight = 12110.159| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.61 r_work: 0.3090 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4404 Z= 0.189 Angle : 0.563 11.994 5961 Z= 0.293 Chirality : 0.041 0.133 650 Planarity : 0.004 0.032 780 Dihedral : 8.998 153.987 603 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.61 % Allowed : 20.92 % Favored : 76.47 % 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 (0.38), residues: 536 helix: 0.97 (0.32), residues: 294 sheet: -0.61 (0.75), residues: 43 loop : 0.61 (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 0.010 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 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.418 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.9845 time to fit residues: 43.8580 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 867 THR 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 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 955 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.070839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062271 restraints weight = 12332.983| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.67 r_work: 0.3102 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4404 Z= 0.170 Angle : 0.555 12.204 5961 Z= 0.290 Chirality : 0.041 0.158 650 Planarity : 0.004 0.031 780 Dihedral : 8.874 152.937 603 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.40 % Allowed : 20.70 % 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: 1.02 (0.38), residues: 536 helix: 1.02 (0.32), residues: 294 sheet: -0.58 (0.75), 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 0.010 0.001 PHE A 879 TYR 0.012 0.001 TYR A 853 ARG 0.003 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 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 852 MET cc_start: 0.8715 (tpp) cc_final: 0.8324 (tpt) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 1.0648 time to fit residues: 48.1685 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR 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 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 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 GLN A 955 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061334 restraints weight = 12097.856| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.64 r_work: 0.3081 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1951 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= 0.209 Angle : 0.597 12.284 5961 Z= 0.314 Chirality : 0.042 0.181 650 Planarity : 0.004 0.032 780 Dihedral : 8.997 153.777 603 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.96 % Allowed : 20.92 % 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: 0.95 (0.32), residues: 294 sheet: -0.60 (0.74), residues: 43 loop : 0.68 (0.47), 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 0.011 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 42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 852 MET cc_start: 0.8605 (tpp) cc_final: 0.8143 (tpt) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 1.0260 time to fit residues: 44.3344 Evaluate side-chains 38 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 599 THR 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 43 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.061353 restraints weight = 12259.941| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.65 r_work: 0.3080 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1942 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= 0.217 Angle : 0.611 11.973 5961 Z= 0.324 Chirality : 0.042 0.183 650 Planarity : 0.004 0.032 780 Dihedral : 9.024 153.973 603 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.18 % Allowed : 21.13 % 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: 0.93 (0.38), residues: 536 helix: 0.94 (0.32), residues: 294 sheet: -0.59 (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 0.004 0.001 HIS A 536 PHE 0.012 0.001 PHE A 879 TYR 0.015 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: 3118.02 seconds wall clock time: 55 minutes 59.47 seconds (3359.47 seconds total)