Starting phenix.real_space_refine on Thu Jul 2 01:17:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz1_15031/07_2026/7zz1_15031.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 0.86, per 1000 atoms: 0.17 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: 0.28 Conformation dependent library (CDL) restraints added in 115.2 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: 0.09 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: 0.50 Time building geometry restraints manager: 0.36 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: 2829 29.67 - 59.34: 168 59.34 - 89.00: 19 89.00 - 118.67: 0 118.67 - 148.34: 1 Dihedral angle restraints: 3017 sinusoidal: 1232 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 3014 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: 1.450 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:5.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 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 : 18.213 148.341 1873 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 are 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/Z covalent geometry : bond 0.00721 / 0.34 ( 5000) covalent geometry : angle 0.89477 / 0.47 ( 6764) hydrogen bonds : bond 0.20161 / 14.13 ( 224) hydrogen bonds : angle 8.34646 / 5.77 ( 642) Misc. bond : bond 0.00018 / 0.01 ( 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 : 0.112 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.4328 time to fit residues: 30.1512 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 : 0.112 ------------------------------------------------------------------------------- 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... A 749 GLN A 832 ASN A 882 GLN B1128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.067745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055438 restraints weight = 14529.218| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.92 r_work: 0.3051 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 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= 0.118 Angle : 0.531 5.777 6764 Z= 0.281 Chirality : 0.041 0.145 749 Planarity : 0.004 0.035 883 Dihedral : 9.057 152.323 700 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 19.92 % Favored : 77.01 % 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 are not related in a simple way. whole: 0.27 (0.33), residues: 611 helix: 0.90 (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/Z covalent geometry : bond 0.00259 / 0.12 ( 5000) covalent geometry : angle 0.53123 / 0.28 ( 6764) hydrogen bonds : bond 0.04191 / 2.92 ( 224) hydrogen bonds : angle 5.83081 / 4.04 ( 642) Misc. bond : bond 0.00002 / 0.00 ( 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 : 0.113 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8809 (mppt) cc_final: 0.8560 (mppt) outliers start: 16 outliers final: 7 residues processed: 62 average time/residue: 0.4571 time to fit residues: 29.4853 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 : 0.154 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054052 restraints weight = 14341.970| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.90 r_work: 0.3011 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5001 Z= 0.167 Angle : 0.562 9.425 6764 Z= 0.293 Chirality : 0.042 0.157 749 Planarity : 0.004 0.033 883 Dihedral : 8.399 151.902 684 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.26 % Allowed : 19.73 % Favored : 77.01 % 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 are not related in a simple way. whole: 0.74 (0.34), residues: 611 helix: 1.45 (0.31), residues: 289 sheet: -0.51 (0.71), residues: 43 loop : -0.31 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 854 TYR 0.014 0.002 TYR A 853 PHE 0.009 0.001 PHE A 907 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 5000) covalent geometry : angle 0.56165 / 0.29 ( 6764) hydrogen bonds : bond 0.04569 / 3.17 ( 224) hydrogen bonds : angle 5.66550 / 3.92 ( 642) Misc. bond : bond 0.00036 / 0.02 ( 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 67 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.117 Fit side-chains REVERT: B 1075 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6943 (mmt) REVERT: B 1123 LYS cc_start: 0.8865 (mppt) cc_final: 0.8640 (mppt) outliers start: 17 outliers final: 9 residues processed: 59 average time/residue: 0.4665 time to fit residues: 28.6195 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 : 0.114 ------------------------------------------------------------------------------- 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 1071 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 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: 0.7980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053147 restraints weight = 14354.340| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.89 r_work: 0.2981 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5001 Z= 0.224 Angle : 0.593 6.642 6764 Z= 0.312 Chirality : 0.044 0.162 749 Planarity : 0.004 0.034 883 Dihedral : 8.719 154.661 684 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.21 % Allowed : 19.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.34), residues: 611 helix: 1.55 (0.31), residues: 289 sheet: -0.48 (0.72), residues: 43 loop : -0.27 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 854 TYR 0.016 0.002 TYR A 853 PHE 0.010 0.001 PHE A 907 TRP 0.008 0.002 TRP A 569 HIS 0.007 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 5000) covalent geometry : angle 0.59278 / 0.31 ( 6764) hydrogen bonds : bond 0.05022 / 3.48 ( 224) hydrogen bonds : angle 5.73144 / 3.97 ( 642) Misc. bond : bond 0.00051 / 0.03 ( 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 76 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.131 Fit side-chains REVERT: A 705 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.9234 (pmm) outliers start: 22 outliers final: 10 residues processed: 67 average time/residue: 0.4818 time to fit residues: 33.6194 Evaluate side-chains 63 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054616 restraints weight = 14773.963| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.74 r_work: 0.3010 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5001 Z= 0.149 Angle : 0.555 6.424 6764 Z= 0.291 Chirality : 0.042 0.155 749 Planarity : 0.003 0.033 883 Dihedral : 8.568 156.800 684 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.64 % Allowed : 20.31 % 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 are not related in a simple way. whole: 0.99 (0.35), residues: 611 helix: 1.72 (0.31), residues: 290 sheet: -0.58 (0.71), residues: 43 loop : -0.22 (0.39), residues: 278 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 879 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 5000) covalent geometry : angle 0.55485 / 0.29 ( 6764) hydrogen bonds : bond 0.04215 / 2.92 ( 224) hydrogen bonds : angle 5.51099 / 3.81 ( 642) Misc. bond : bond 0.00030 / 0.02 ( 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: 19 poor density : 52 time to evaluate : 0.159 Fit side-chains REVERT: B 1118 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (p0) outliers start: 19 outliers final: 9 residues processed: 63 average time/residue: 0.4594 time to fit residues: 30.1227 Evaluate side-chains 61 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054541 restraints weight = 14839.672| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.75 r_work: 0.3015 rms_B_bonded: 2.11 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: 0.8984 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5001 Z= 0.154 Angle : 0.572 10.307 6764 Z= 0.295 Chirality : 0.042 0.156 749 Planarity : 0.003 0.032 883 Dihedral : 8.518 156.575 684 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.26 % Allowed : 21.07 % 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 are not related in a simple way. whole: 1.00 (0.35), residues: 611 helix: 1.75 (0.31), residues: 290 sheet: -0.62 (0.71), residues: 43 loop : -0.23 (0.39), residues: 278 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 0.009 0.001 PHE A 879 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 5000) covalent geometry : angle 0.57177 / 0.29 ( 6764) hydrogen bonds : bond 0.04243 / 2.94 ( 224) hydrogen bonds : angle 5.48739 / 3.79 ( 642) Misc. bond : bond 0.00026 / 0.01 ( 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 70 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.131 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 0.4693 time to fit residues: 30.8073 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 : 0.115 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.070475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058409 restraints weight = 14561.549| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.78 r_work: 0.3013 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1472 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 : 0.582 9.511 6764 Z= 0.303 Chirality : 0.043 0.230 749 Planarity : 0.004 0.031 883 Dihedral : 8.509 156.632 684 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.26 % Allowed : 21.07 % 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 are not related in a simple way. whole: 1.01 (0.35), residues: 611 helix: 1.79 (0.31), residues: 290 sheet: -0.64 (0.70), residues: 43 loop : -0.26 (0.39), residues: 278 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 0.030 0.002 PHE A 846 TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5000) covalent geometry : angle 0.58178 / 0.30 ( 6764) hydrogen bonds : bond 0.04135 / 2.87 ( 224) hydrogen bonds : angle 5.41647 / 3.75 ( 642) Misc. bond : bond 0.00026 / 0.01 ( 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 68 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.132 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8906 (mppt) cc_final: 0.8681 (mppt) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.4903 time to fit residues: 32.0744 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN A 817 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058488 restraints weight = 14819.865| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.79 r_work: 0.3014 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5001 Z= 0.153 Angle : 0.575 8.315 6764 Z= 0.300 Chirality : 0.043 0.221 749 Planarity : 0.004 0.031 883 Dihedral : 8.500 156.431 684 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.35), residues: 611 helix: 1.81 (0.31), residues: 288 sheet: -0.64 (0.71), 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 0.015 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/Z covalent geometry : bond 0.00352 / 0.15 ( 5000) covalent geometry : angle 0.57524 / 0.30 ( 6764) hydrogen bonds : bond 0.04151 / 2.88 ( 224) hydrogen bonds : angle 5.42200 / 3.75 ( 642) Misc. bond : bond 0.00029 / 0.02 ( 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 : 0.113 Fit side-chains REVERT: B 1123 LYS cc_start: 0.8888 (mppt) cc_final: 0.8686 (mppt) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.4595 time to fit residues: 28.6843 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN B1128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054559 restraints weight = 14449.690| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1566 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= 0.135 Angle : 0.593 10.842 6764 Z= 0.304 Chirality : 0.042 0.205 749 Planarity : 0.003 0.030 883 Dihedral : 8.444 156.532 684 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 are not related in a simple way. whole: 1.02 (0.35), residues: 611 helix: 1.82 (0.31), residues: 288 sheet: -0.66 (0.72), residues: 43 loop : -0.28 (0.38), residues: 280 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 0.014 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/Z covalent geometry : bond 0.00311 / 0.13 ( 5000) covalent geometry : angle 0.59262 / 0.30 ( 6764) hydrogen bonds : bond 0.03890 / 2.70 ( 224) hydrogen bonds : angle 5.34391 / 3.69 ( 642) Misc. bond : bond 0.00013 / 0.01 ( 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 62 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.196 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.5673 time to fit residues: 33.7180 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN 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 = 0.066545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054759 restraints weight = 14815.998| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.75 r_work: 0.3017 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5001 Z= 0.155 Angle : 0.609 9.839 6764 Z= 0.313 Chirality : 0.043 0.205 749 Planarity : 0.004 0.031 883 Dihedral : 8.482 156.180 684 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.49 % Allowed : 21.84 % 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 are not related in a simple way. whole: 0.97 (0.35), residues: 611 helix: 1.78 (0.31), residues: 288 sheet: -0.69 (0.71), residues: 43 loop : -0.30 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 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/Z covalent geometry : bond 0.00360 / 0.16 ( 5000) covalent geometry : angle 0.60861 / 0.31 ( 6764) hydrogen bonds : bond 0.04141 / 2.87 ( 224) hydrogen bonds : angle 5.41709 / 3.74 ( 642) Misc. bond : bond 0.00026 / 0.01 ( 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 61 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.131 Fit side-chains REVERT: A 705 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9222 (pmm) REVERT: B 1094 GLN cc_start: 0.8506 (tp40) cc_final: 0.8216 (tp40) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.5969 time to fit residues: 34.7567 Evaluate side-chains 58 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 27 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055603 restraints weight = 15105.318| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.78 r_work: 0.3035 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1612 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= 0.128 Angle : 0.585 10.356 6764 Z= 0.301 Chirality : 0.042 0.194 749 Planarity : 0.003 0.030 883 Dihedral : 8.388 156.489 684 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.30 % Allowed : 22.03 % 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 are not related in a simple way. whole: 0.99 (0.35), residues: 611 helix: 1.82 (0.31), residues: 288 sheet: -0.69 (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 0.011 0.001 TYR A 853 PHE 0.012 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/Z covalent geometry : bond 0.00295 / 0.13 ( 5000) covalent geometry : angle 0.58548 / 0.30 ( 6764) hydrogen bonds : bond 0.03749 / 2.60 ( 224) hydrogen bonds : angle 5.29249 / 3.66 ( 642) Misc. bond : bond 0.00005 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.79 seconds wall clock time: 30 minutes 28.75 seconds (1828.75 seconds total)