Starting phenix.real_space_refine on Fri Dec 27 13:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz1_15031/12_2024/7zz1_15031.cif" } resolution = 2.27 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Mg 1 5.21 5 S 24 5.16 5 C 3110 2.51 5 N 829 2.21 5 O 993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4958 Number of models: 1 Model: "" Number of chains: 5 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: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 576 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 1, ' MN': 1, 'OAA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Time building chain proxies: 4.00, per 1000 atoms: 0.81 Number of scatterers: 4958 At special positions: 0 Unit cell: (69.96, 76.32, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 24 16.00 Mg 1 11.99 O 993 8.00 N 829 7.00 C 3110 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 700.2 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 4 sheets defined 54.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.512A pdb=" N MET A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.873A 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 606 through 610 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.640A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.503A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.648A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.934A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.853A 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 819 through 824 Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 829 through 840 removed outlier: 3.527A pdb=" N LYS A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 861 Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 886 through 894 removed outlier: 3.517A pdb=" N TYR A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 945 through 958 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 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: 6.764A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 733 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1070 through 1072 removed outlier: 8.202A pdb=" N LEU B1133 " --> pdb=" O LEU B1119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU B1119 " --> pdb=" O LEU B1133 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU B1135 " --> pdb=" O VAL B1117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B1117 " --> pdb=" O GLU B1135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1077 through 1078 Processing sheet with id=AA4, first strand: chain 'B' and resid 1097 through 1100 removed outlier: 4.174A pdb=" N MET B1097 " --> pdb=" O ILE B1108 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 642 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: 1.33 Time building geometry restraints manager: 1.52 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: 1630 1.34 - 1.46: 1030 1.46 - 1.58: 2293 1.58 - 1.70: 1 1.70 - 1.82: 46 Bond restraints: 5000 Sorted by residual: bond pdb=" C3 BTN B1201 " pdb=" O3 BTN B1201 " ideal model delta sigma weight residual 1.220 1.409 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C2 BTN B1201 " pdb=" S1 BTN B1201 " ideal model delta sigma weight residual 1.824 1.671 0.153 2.00e-02 2.50e+03 5.88e+01 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 A1203 " pdb=" O3 OAA A1203 " ideal model delta sigma weight residual 1.214 1.306 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 4995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 6589 2.45 - 4.91: 140 4.91 - 7.36: 28 7.36 - 9.81: 4 9.81 - 12.26: 3 Bond angle restraints: 6764 Sorted by residual: angle pdb=" CA GLN B1130 " pdb=" CB GLN B1130 " pdb=" CG GLN B1130 " ideal model delta sigma weight residual 114.10 125.45 -11.35 2.00e+00 2.50e-01 3.22e+01 angle pdb=" CA LYS B1062 " pdb=" CB LYS B1062 " pdb=" CG LYS B1062 " ideal model delta sigma weight residual 114.10 124.11 -10.01 2.00e+00 2.50e-01 2.50e+01 angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 115.88 7.12 1.60e+00 3.91e-01 1.98e+01 angle pdb=" CA GLU B1064 " pdb=" CB GLU B1064 " pdb=" CG GLU B1064 " ideal model delta sigma weight residual 114.10 122.37 -8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CB GLN B1094 " pdb=" CG GLN B1094 " pdb=" CD GLN B1094 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.70e+00 3.46e-01 1.43e+01 ... (remaining 6759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.67: 2842 29.67 - 59.34: 170 59.34 - 89.00: 19 89.00 - 118.67: 0 118.67 - 148.34: 1 Dihedral angle restraints: 3032 sinusoidal: 1247 harmonic: 1785 Sorted by residual: dihedral pdb=" C1 OAA A1203 " pdb=" C2 OAA A1203 " pdb=" C3 OAA A1203 " pdb=" O3 OAA A1203 " ideal model delta sinusoidal sigma weight residual -102.23 46.11 -148.34 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA LYS B1123 " pdb=" C LYS B1123 " pdb=" N GLY B1124 " pdb=" CA GLY B1124 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA THR A 886 " pdb=" C THR A 886 " pdb=" N GLU A 887 " pdb=" CA GLU A 887 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 538 0.046 - 0.092: 163 0.092 - 0.139: 39 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 749 Sorted by residual: chirality pdb=" CB ILE A 813 " pdb=" CA ILE A 813 " pdb=" CG1 ILE A 813 " pdb=" CG2 ILE A 813 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2 BTN B1201 " pdb=" C4 BTN B1201 " pdb=" C7 BTN B1201 " pdb=" S1 BTN B1201 " both_signs ideal model delta sigma weight residual False 3.08 2.87 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL B1084 " pdb=" CA VAL B1084 " pdb=" CG1 VAL B1084 " pdb=" CG2 VAL B1084 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 746 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.032 2.00e-02 2.50e+03 5.86e-02 3.43e+01 pdb=" C VAL A 702 " -0.101 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.038 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B1130 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLN B1130 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN B1130 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B1131 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1098 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL B1098 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B1098 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B1099 " -0.012 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 223 2.71 - 3.26: 4973 3.26 - 3.80: 9171 3.80 - 4.35: 11387 4.35 - 4.90: 18305 Nonbonded interactions: 44059 Sorted by model distance: nonbonded pdb=" OQ1 KCX A 703 " pdb="MN MN A1202 " model vdw 2.159 2.320 nonbonded pdb="MN MN A1202 " pdb=" O HOH A1330 " model vdw 2.162 2.320 nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1202 " model vdw 2.195 2.320 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1202 " model vdw 2.216 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1202 " model vdw 2.235 2.400 ... (remaining 44054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.050 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 0.189 5000 Z= 0.429 Angle : 0.895 12.264 6764 Z= 0.474 Chirality : 0.048 0.231 749 Planarity : 0.006 0.062 883 Dihedral : 18.254 148.341 1888 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.68 % Allowed : 21.65 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.05 (0.31), residues: 611 helix: -0.74 (0.26), residues: 285 sheet: -0.04 (0.74), residues: 43 loop : -0.59 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 799 HIS 0.010 0.001 HIS A 823 PHE 0.013 0.002 PHE A 907 TYR 0.015 0.002 TYR A 853 ARG 0.014 0.001 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.547 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 1.4913 time to fit residues: 103.8905 Evaluate side-chains 63 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1088 ASP Chi-restraints excluded: chain B residue 1099 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 GLN B1128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5000 Z= 0.191 Angle : 0.542 5.841 6764 Z= 0.288 Chirality : 0.041 0.147 749 Planarity : 0.004 0.036 883 Dihedral : 9.066 152.066 715 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.26 % Allowed : 19.54 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.26 (0.33), residues: 611 helix: 0.88 (0.29), residues: 289 sheet: -0.31 (0.71), residues: 43 loop : -0.41 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.007 0.001 HIS A 823 PHE 0.011 0.001 PHE A 907 TYR 0.010 0.001 TYR A 853 ARG 0.007 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.625 Fit side-chains REVERT: B 1075 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: B 1123 LYS cc_start: 0.8738 (mppt) cc_final: 0.8510 (mppt) outliers start: 17 outliers final: 7 residues processed: 62 average time/residue: 1.3962 time to fit residues: 90.1391 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.0060 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5000 Z= 0.150 Angle : 0.525 10.075 6764 Z= 0.272 Chirality : 0.040 0.151 749 Planarity : 0.003 0.031 883 Dihedral : 8.451 150.810 699 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.07 % Allowed : 19.35 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.73 (0.34), residues: 611 helix: 1.46 (0.30), residues: 290 sheet: -0.50 (0.72), residues: 43 loop : -0.33 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.009 0.001 PHE A 907 TYR 0.011 0.001 TYR A 853 ARG 0.005 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.558 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 1.3169 time to fit residues: 86.7197 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5000 Z= 0.264 Angle : 0.568 9.751 6764 Z= 0.296 Chirality : 0.043 0.157 749 Planarity : 0.004 0.031 883 Dihedral : 8.675 152.089 699 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.64 % Allowed : 19.73 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.89 (0.34), residues: 611 helix: 1.65 (0.31), residues: 289 sheet: -0.49 (0.73), residues: 43 loop : -0.31 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.029 0.002 PHE A 846 TYR 0.014 0.002 TYR A 853 ARG 0.004 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.581 Fit side-chains REVERT: B 1075 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7090 (mmt) outliers start: 19 outliers final: 8 residues processed: 63 average time/residue: 1.3733 time to fit residues: 90.2357 Evaluate side-chains 59 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5000 Z= 0.258 Angle : 0.577 8.650 6764 Z= 0.301 Chirality : 0.042 0.157 749 Planarity : 0.003 0.031 883 Dihedral : 8.754 153.845 699 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.83 % Allowed : 20.50 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.95 (0.35), residues: 611 helix: 1.72 (0.31), residues: 288 sheet: -0.60 (0.72), residues: 43 loop : -0.27 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.013 0.001 PHE A 846 TYR 0.013 0.002 TYR A 853 ARG 0.004 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.806 Fit side-chains REVERT: A 876 MET cc_start: 0.9105 (tpt) cc_final: 0.8900 (tpt) REVERT: B 1075 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7123 (mmt) REVERT: B 1118 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7420 (p0) outliers start: 20 outliers final: 11 residues processed: 64 average time/residue: 1.4710 time to fit residues: 98.3001 Evaluate side-chains 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 600 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5000 Z= 0.186 Angle : 0.557 10.539 6764 Z= 0.285 Chirality : 0.041 0.152 749 Planarity : 0.003 0.031 883 Dihedral : 8.580 154.897 699 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.64 % Allowed : 20.88 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.98 (0.35), residues: 611 helix: 1.78 (0.31), residues: 289 sheet: -0.63 (0.72), residues: 43 loop : -0.29 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.010 0.001 PHE A 846 TYR 0.011 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.833 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 62 average time/residue: 1.8073 time to fit residues: 116.6104 Evaluate side-chains 59 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A 817 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5000 Z= 0.316 Angle : 0.615 9.744 6764 Z= 0.321 Chirality : 0.045 0.304 749 Planarity : 0.004 0.033 883 Dihedral : 8.875 153.927 699 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.26 % Allowed : 20.88 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.35), residues: 611 helix: 1.69 (0.31), residues: 290 sheet: -0.66 (0.70), residues: 43 loop : -0.25 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.013 0.002 PHE A 846 TYR 0.015 0.002 TYR A 853 ARG 0.003 0.001 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.619 Fit side-chains REVERT: A 705 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9272 (pmm) REVERT: A 876 MET cc_start: 0.9120 (tpt) cc_final: 0.8910 (tpt) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 1.3941 time to fit residues: 88.7771 Evaluate side-chains 60 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5000 Z= 0.215 Angle : 0.568 8.642 6764 Z= 0.295 Chirality : 0.043 0.278 749 Planarity : 0.003 0.031 883 Dihedral : 8.722 155.670 699 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 21.07 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.03 (0.35), residues: 611 helix: 1.81 (0.31), residues: 288 sheet: -0.70 (0.70), residues: 43 loop : -0.23 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.011 0.001 PHE A 846 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.592 Fit side-chains REVERT: A 705 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9252 (pmm) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 1.5806 time to fit residues: 98.6904 Evaluate side-chains 60 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5000 Z= 0.247 Angle : 0.599 8.918 6764 Z= 0.311 Chirality : 0.043 0.273 749 Planarity : 0.004 0.031 883 Dihedral : 8.764 155.150 699 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.45 % Allowed : 20.11 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.01 (0.35), residues: 611 helix: 1.79 (0.31), residues: 288 sheet: -0.72 (0.71), residues: 43 loop : -0.23 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.011 0.001 PHE A 846 TYR 0.013 0.002 TYR A 853 ARG 0.003 0.000 ARG B1061 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.648 Fit side-chains REVERT: A 705 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9260 (pmm) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 1.6694 time to fit residues: 107.9093 Evaluate side-chains 61 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 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 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5000 Z= 0.216 Angle : 0.607 8.477 6764 Z= 0.314 Chirality : 0.043 0.255 749 Planarity : 0.003 0.031 883 Dihedral : 8.696 155.774 699 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.49 % Allowed : 21.26 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.35), residues: 611 helix: 1.81 (0.31), residues: 288 sheet: -0.75 (0.71), residues: 43 loop : -0.23 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 PHE 0.010 0.001 PHE A 846 TYR 0.012 0.001 TYR A 853 ARG 0.003 0.000 ARG A 854 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.572 Fit side-chains REVERT: A 705 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.9230 (pmm) REVERT: B 1094 GLN cc_start: 0.8549 (tp40) cc_final: 0.8219 (tp40) outliers start: 13 outliers final: 11 residues processed: 58 average time/residue: 1.4888 time to fit residues: 89.9863 Evaluate side-chains 61 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1079 VAL Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054659 restraints weight = 14615.068| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.74 r_work: 0.3014 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5000 Z= 0.247 Angle : 0.613 8.517 6764 Z= 0.317 Chirality : 0.043 0.248 749 Planarity : 0.004 0.031 883 Dihedral : 8.766 155.267 699 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.68 % Allowed : 20.69 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.98 (0.35), residues: 611 helix: 1.77 (0.31), residues: 288 sheet: -0.76 (0.71), residues: 43 loop : -0.24 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 PHE 0.011 0.001 PHE A 846 TYR 0.013 0.001 TYR A 853 ARG 0.003 0.000 ARG B1061 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.39 seconds wall clock time: 43 minutes 4.44 seconds (2584.44 seconds total)