Starting phenix.real_space_refine on Fri Aug 22 15:41:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz1_15031/08_2025/7zz1_15031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz1_15031/08_2025/7zz1_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_15031/08_2025/7zz1_15031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz1_15031/08_2025/7zz1_15031.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz1_15031/08_2025/7zz1_15031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz1_15031/08_2025/7zz1_15031.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.30 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: 0.55 Conformation dependent library (CDL) restraints added in 184.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.19 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: 0.79 Time building geometry restraints manager: 0.59 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: 1.860 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.930 Find NCS groups from input model: 0.020 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- 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 5001 Z= 0.342 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG A 854 TYR 0.015 0.002 TYR A 853 PHE 0.013 0.002 PHE A 907 TRP 0.009 0.002 TRP A 799 HIS 0.010 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00721 ( 5000) covalent geometry : angle 0.89477 ( 6764) hydrogen bonds : bond 0.20161 ( 224) hydrogen bonds : angle 8.34646 ( 642) Misc. bond : bond 0.00018 ( 1) *********************** 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 : 0.217 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.6619 time to fit residues: 46.0624 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 : 0.248 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.067774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055459 restraints weight = 14523.336| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.92 r_work: 0.3052 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5001 Z= 0.117 Angle : 0.531 5.920 6764 Z= 0.281 Chirality : 0.041 0.145 749 Planarity : 0.004 0.034 883 Dihedral : 8.955 152.045 715 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 19.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.33), residues: 611 helix: 0.88 (0.29), residues: 289 sheet: -0.33 (0.71), residues: 43 loop : -0.41 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 854 TYR 0.010 0.001 TYR A 853 PHE 0.011 0.001 PHE A 907 TRP 0.005 0.001 TRP A 569 HIS 0.007 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5000) covalent geometry : angle 0.53065 ( 6764) hydrogen bonds : bond 0.04215 ( 224) hydrogen bonds : angle 5.82729 ( 642) Misc. bond : bond 0.00010 ( 1) *********************** 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 68 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.216 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8814 (mppt) cc_final: 0.8564 (mppt) outliers start: 16 outliers final: 7 residues processed: 62 average time/residue: 0.6014 time to fit residues: 38.8890 Evaluate side-chains 55 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.0010 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054879 restraints weight = 14387.011| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.91 r_work: 0.3034 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5001 Z= 0.131 Angle : 0.539 9.451 6764 Z= 0.280 Chirality : 0.041 0.155 749 Planarity : 0.003 0.032 883 Dihedral : 8.555 150.703 699 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.07 % Allowed : 19.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.34), residues: 611 helix: 1.49 (0.31), residues: 289 sheet: -0.51 (0.71), residues: 43 loop : -0.32 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 854 TYR 0.012 0.001 TYR A 853 PHE 0.009 0.001 PHE A 907 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5000) covalent geometry : angle 0.53881 ( 6764) hydrogen bonds : bond 0.04157 ( 224) hydrogen bonds : angle 5.55463 ( 642) Misc. bond : bond 0.00010 ( 1) *********************** 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 66 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.195 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8790 (mppt) cc_final: 0.8544 (mppt) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.6586 time to fit residues: 40.3722 Evaluate side-chains 57 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.066663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054245 restraints weight = 14406.976| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.91 r_work: 0.3014 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5001 Z= 0.152 Angle : 0.536 6.524 6764 Z= 0.282 Chirality : 0.042 0.155 749 Planarity : 0.003 0.031 883 Dihedral : 8.638 152.776 699 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.02 % Allowed : 18.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.35), residues: 611 helix: 1.68 (0.31), residues: 289 sheet: -0.51 (0.72), residues: 43 loop : -0.34 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 854 TYR 0.013 0.001 TYR A 853 PHE 0.009 0.001 PHE A 907 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5000) covalent geometry : angle 0.53597 ( 6764) hydrogen bonds : bond 0.04279 ( 224) hydrogen bonds : angle 5.51218 ( 642) Misc. bond : bond 0.00016 ( 1) *********************** 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 74 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.129 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 65 average time/residue: 0.5881 time to fit residues: 39.7778 Evaluate side-chains 57 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 819 GLU 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 1107 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055173 restraints weight = 14570.638| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.94 r_work: 0.3045 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5001 Z= 0.116 Angle : 0.528 6.482 6764 Z= 0.276 Chirality : 0.041 0.150 749 Planarity : 0.003 0.028 883 Dihedral : 8.501 153.607 699 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 20.11 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.34), residues: 611 helix: 1.78 (0.31), residues: 289 sheet: -0.54 (0.74), residues: 43 loop : -0.34 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.011 0.001 TYR A 853 PHE 0.024 0.001 PHE A 846 TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5000) covalent geometry : angle 0.52777 ( 6764) hydrogen bonds : bond 0.03721 ( 224) hydrogen bonds : angle 5.30910 ( 642) Misc. bond : bond 0.00000 ( 1) *********************** 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: 16 poor density : 55 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 1118 ASP cc_start: 0.7474 (p0) cc_final: 0.7126 (p0) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.6347 time to fit residues: 43.5990 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 : 0.133 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A 844 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.066976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055070 restraints weight = 14898.886| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.75 r_work: 0.3027 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5001 Z= 0.139 Angle : 0.545 9.907 6764 Z= 0.282 Chirality : 0.041 0.153 749 Planarity : 0.003 0.029 883 Dihedral : 8.554 153.473 699 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.02 % Allowed : 19.92 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.35), residues: 611 helix: 1.82 (0.31), residues: 289 sheet: -0.55 (0.73), residues: 43 loop : -0.35 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 854 TYR 0.013 0.001 TYR A 853 PHE 0.016 0.001 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5000) covalent geometry : angle 0.54523 ( 6764) hydrogen bonds : bond 0.04019 ( 224) hydrogen bonds : angle 5.37059 ( 642) Misc. bond : bond 0.00009 ( 1) *********************** 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: 21 poor density : 50 time to evaluate : 0.249 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 65 average time/residue: 0.6128 time to fit residues: 41.5500 Evaluate side-chains 60 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.066847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054985 restraints weight = 14801.505| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.75 r_work: 0.3025 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5001 Z= 0.146 Angle : 0.570 9.460 6764 Z= 0.295 Chirality : 0.042 0.152 749 Planarity : 0.003 0.029 883 Dihedral : 8.574 153.932 699 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.07 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.35), residues: 611 helix: 1.83 (0.31), residues: 288 sheet: -0.63 (0.72), residues: 43 loop : -0.30 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1061 TYR 0.012 0.001 TYR A 853 PHE 0.016 0.001 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5000) covalent geometry : angle 0.57026 ( 6764) hydrogen bonds : bond 0.04028 ( 224) hydrogen bonds : angle 5.34759 ( 642) Misc. bond : bond 0.00015 ( 1) *********************** 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 67 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.173 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.5886 time to fit residues: 37.3950 Evaluate side-chains 61 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 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 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.066983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055250 restraints weight = 14967.089| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.76 r_work: 0.3033 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5001 Z= 0.133 Angle : 0.557 8.214 6764 Z= 0.289 Chirality : 0.041 0.151 749 Planarity : 0.003 0.028 883 Dihedral : 8.541 154.006 699 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.07 % Allowed : 20.88 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.35), residues: 611 helix: 1.82 (0.31), residues: 289 sheet: -0.66 (0.72), residues: 43 loop : -0.35 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1061 TYR 0.011 0.001 TYR A 853 PHE 0.015 0.001 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5000) covalent geometry : angle 0.55668 ( 6764) hydrogen bonds : bond 0.03878 ( 224) hydrogen bonds : angle 5.32394 ( 642) Misc. bond : bond 0.00007 ( 1) *********************** 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 : 0.176 Fit side-chains REVERT: B 1062 LYS cc_start: 0.7856 (tmtt) cc_final: 0.7591 (tmmt) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.5657 time to fit residues: 34.7509 Evaluate side-chains 60 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 819 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.067044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055207 restraints weight = 14728.226| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.75 r_work: 0.3036 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5001 Z= 0.138 Angle : 0.581 8.733 6764 Z= 0.300 Chirality : 0.042 0.152 749 Planarity : 0.003 0.028 883 Dihedral : 8.550 154.028 699 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 20.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.35), residues: 611 helix: 1.81 (0.31), residues: 289 sheet: -0.67 (0.72), residues: 43 loop : -0.35 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.011 0.001 TYR A 853 PHE 0.014 0.001 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5000) covalent geometry : angle 0.58080 ( 6764) hydrogen bonds : bond 0.03894 ( 224) hydrogen bonds : angle 5.31450 ( 642) Misc. bond : bond 0.00004 ( 1) *********************** 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: 16 poor density : 52 time to evaluate : 0.200 Fit side-chains REVERT: B 1094 GLN cc_start: 0.8515 (tp40) cc_final: 0.8223 (tp40) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.6272 time to fit residues: 40.5121 Evaluate side-chains 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.066938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055187 restraints weight = 14810.313| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.75 r_work: 0.3030 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5001 Z= 0.143 Angle : 0.582 8.042 6764 Z= 0.301 Chirality : 0.042 0.152 749 Planarity : 0.003 0.028 883 Dihedral : 8.575 154.124 699 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 20.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.35), residues: 611 helix: 1.82 (0.31), residues: 288 sheet: -0.68 (0.72), residues: 43 loop : -0.33 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.011 0.001 TYR A 853 PHE 0.015 0.001 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5000) covalent geometry : angle 0.58167 ( 6764) hydrogen bonds : bond 0.03983 ( 224) hydrogen bonds : angle 5.33594 ( 642) Misc. bond : bond 0.00009 ( 1) ********************** 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 66 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.213 Fit side-chains REVERT: A 705 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.9250 (pmm) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 0.6201 time to fit residues: 38.8347 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 : 0.199 ------------------------------------------------------------------------------- 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4482 > 50: distance: 4 - 8: 3.901 distance: 8 - 9: 14.066 distance: 9 - 10: 12.751 distance: 9 - 12: 21.257 distance: 10 - 11: 21.030 distance: 10 - 17: 24.841 distance: 12 - 13: 15.661 distance: 13 - 14: 13.901 distance: 14 - 15: 6.481 distance: 14 - 16: 7.927 distance: 17 - 18: 19.885 distance: 17 - 23: 24.414 distance: 18 - 19: 3.219 distance: 18 - 21: 3.829 distance: 19 - 20: 14.900 distance: 19 - 24: 17.076 distance: 21 - 22: 28.210 distance: 22 - 23: 8.122 distance: 24 - 25: 15.934 distance: 25 - 26: 14.131 distance: 25 - 28: 15.674 distance: 26 - 27: 28.775 distance: 26 - 35: 16.852 distance: 28 - 29: 26.467 distance: 29 - 30: 23.701 distance: 30 - 31: 30.483 distance: 31 - 32: 8.128 distance: 32 - 33: 9.344 distance: 32 - 34: 9.600 distance: 35 - 36: 20.902 distance: 36 - 37: 9.475 distance: 36 - 39: 14.815 distance: 37 - 38: 15.844 distance: 37 - 44: 8.194 distance: 39 - 40: 25.394 distance: 40 - 41: 15.002 distance: 41 - 42: 14.423 distance: 41 - 43: 35.691 distance: 44 - 45: 21.859 distance: 44 - 50: 19.393 distance: 45 - 46: 8.265 distance: 45 - 48: 24.177 distance: 46 - 47: 14.000 distance: 46 - 51: 9.264 distance: 48 - 49: 13.426 distance: 49 - 50: 33.444 distance: 51 - 52: 9.061 distance: 52 - 53: 7.900 distance: 52 - 55: 8.975 distance: 53 - 54: 8.941 distance: 55 - 56: 8.259 distance: 56 - 57: 7.660 distance: 56 - 58: 6.867 distance: 59 - 60: 5.978 distance: 60 - 61: 8.044 distance: 61 - 62: 8.175 distance: 61 - 67: 5.014 distance: 63 - 64: 4.996 distance: 64 - 65: 6.266 distance: 64 - 66: 3.723 distance: 67 - 68: 25.761 distance: 68 - 69: 6.586 distance: 68 - 71: 20.177 distance: 69 - 70: 37.208 distance: 69 - 75: 12.764 distance: 71 - 72: 17.038 distance: 72 - 73: 18.736 distance: 72 - 74: 7.039 distance: 75 - 76: 8.375 distance: 76 - 77: 3.346 distance: 77 - 78: 12.645 distance: 77 - 83: 11.980 distance: 79 - 80: 7.773 distance: 80 - 81: 9.754 distance: 80 - 82: 5.607 distance: 83 - 84: 26.661 distance: 84 - 85: 4.533 distance: 84 - 87: 22.530 distance: 85 - 86: 18.858 distance: 85 - 92: 3.922 distance: 87 - 88: 8.270 distance: 88 - 89: 7.606 distance: 89 - 90: 11.616 distance: 89 - 91: 13.050