Starting phenix.real_space_refine on Tue Mar 3 12:43:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyz_15029/03_2026/7zyz_15029.map" } resolution = 2.47 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 19 5.16 5 C 2740 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4349 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4301 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 48 Unusual residues: {' MN': 1, 'OAA': 1} Classifications: {'undetermined': 2, 'water': 38} Link IDs: {None: 39} Time building chain proxies: 1.14, per 1000 atoms: 0.26 Number of scatterers: 4349 At special positions: 0 Unit cell: (73.14, 77.38, 80.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 19 16.00 O 858 8.00 N 731 7.00 C 2740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 325.7 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 60.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 502 through 522 removed outlier: 8.050A pdb=" N ALA A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ASP A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.713A pdb=" N GLY A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.801A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 631 Processing helix chain 'A' and resid 644 through 647 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.567A pdb=" N TYR A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.518A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.907A pdb=" N VAL A 820 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 836 Processing helix chain 'A' and resid 845 through 860 removed outlier: 4.077A pdb=" N GLN A 851 " --> pdb=" O ASP A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.714A pdb=" N VAL A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 927 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 945 through 958 removed outlier: 3.908A pdb=" N LYS A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 986 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 1000 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.773A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 601 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 637 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET A 603 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 636 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 665 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 638 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N CYS A 667 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 662 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N KCX A 703 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 666 " --> pdb=" O KCX A 703 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A 733 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 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: 1426 1.34 - 1.46: 731 1.46 - 1.57: 2210 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4404 Sorted by residual: bond pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 1.329 1.427 -0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sigma weight residual 1.214 1.307 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 OAA A1202 " pdb=" O2 OAA A1202 " ideal model delta sigma weight residual 1.242 1.311 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 OAA A1202 " pdb=" O4 OAA A1202 " ideal model delta sigma weight residual 1.241 1.308 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 4399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.66: 5958 7.66 - 15.32: 2 15.32 - 22.98: 0 22.98 - 30.64: 0 30.64 - 38.30: 1 Bond angle restraints: 5961 Sorted by residual: angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 84.70 38.30 1.60e+00 3.91e-01 5.73e+02 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA LYS A 501 " pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.28e+00 angle pdb=" N ALA A 837 " pdb=" CA ALA A 837 " pdb=" C ALA A 837 " ideal model delta sigma weight residual 112.72 109.10 3.62 1.28e+00 6.10e-01 7.99e+00 ... (remaining 5956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2517 32.62 - 65.24: 118 65.24 - 97.86: 13 97.86 - 130.48: 0 130.48 - 163.10: 1 Dihedral angle restraints: 2649 sinusoidal: 1080 harmonic: 1569 Sorted by residual: dihedral pdb=" C1 OAA A1202 " pdb=" C2 OAA A1202 " pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sinusoidal sigma weight residual -102.23 60.87 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA ASN A 609 " pdb=" C ASN A 609 " pdb=" N ALA A 610 " pdb=" CA ALA A 610 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 648 " pdb=" C MET A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 322 0.031 - 0.062: 203 0.062 - 0.093: 90 0.093 - 0.124: 28 0.124 - 0.155: 7 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA LYS A 500 " pdb=" N LYS A 500 " pdb=" C LYS A 500 " pdb=" CB LYS A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA THR A 994 " pdb=" N THR A 994 " pdb=" C THR A 994 " pdb=" CB THR A 994 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 647 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.143 2.00e-02 2.50e+03 2.27e-01 5.14e+02 pdb=" C VAL A 702 " -0.390 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.156 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 501 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LYS A 501 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 501 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 502 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 867 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 868 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 868 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 868 " -0.019 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 60 2.56 - 3.14: 3618 3.14 - 3.73: 7536 3.73 - 4.31: 10651 4.31 - 4.90: 16713 Nonbonded interactions: 38578 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1201 " model vdw 1.973 2.320 nonbonded pdb="MN MN A1201 " pdb=" O HOH A1320 " model vdw 2.002 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1201 " model vdw 2.030 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1201 " model vdw 2.143 2.320 nonbonded pdb=" O HIS A 823 " pdb=" ND1 HIS A 823 " model vdw 2.151 3.120 ... (remaining 38573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.900 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 4404 Z= 0.345 Angle : 0.871 38.295 5961 Z= 0.491 Chirality : 0.047 0.155 650 Planarity : 0.009 0.227 780 Dihedral : 18.664 163.102 1645 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.45 % Allowed : 18.95 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.23 (0.36), residues: 536 helix: -0.09 (0.30), residues: 294 sheet: -0.53 (0.73), residues: 43 loop : 0.14 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 626 TYR 0.013 0.002 TYR A 715 PHE 0.018 0.002 PHE A 879 TRP 0.006 0.002 TRP A 799 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00749 ( 4404) covalent geometry : angle 0.87053 ( 5961) hydrogen bonds : bond 0.19837 ( 200) hydrogen bonds : angle 8.21298 ( 567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.174 Fit side-chains REVERT: A 460 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.5987 (mmt-90) outliers start: 25 outliers final: 24 residues processed: 60 average time/residue: 0.4914 time to fit residues: 30.7215 Evaluate side-chains 58 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.069605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061076 restraints weight = 12212.069| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.60 r_work: 0.3071 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4404 Z= 0.128 Angle : 0.518 6.631 5961 Z= 0.282 Chirality : 0.041 0.131 650 Planarity : 0.004 0.035 780 Dihedral : 10.752 159.781 644 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.14 % Allowed : 18.74 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.37), residues: 536 helix: 0.57 (0.30), residues: 294 sheet: -0.46 (0.71), residues: 43 loop : 0.65 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 803 TYR 0.010 0.001 TYR A 853 PHE 0.015 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4404) covalent geometry : angle 0.51785 ( 5961) hydrogen bonds : bond 0.04529 ( 200) hydrogen bonds : angle 5.70789 ( 567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.196 Fit side-chains REVERT: A 852 MET cc_start: 0.8848 (tpt) cc_final: 0.8528 (tpp) outliers start: 19 outliers final: 4 residues processed: 50 average time/residue: 0.4933 time to fit residues: 25.7342 Evaluate side-chains 36 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 733 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 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 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060734 restraints weight = 12040.828| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.63 r_work: 0.3064 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4404 Z= 0.143 Angle : 0.534 9.829 5961 Z= 0.284 Chirality : 0.042 0.134 650 Planarity : 0.004 0.033 780 Dihedral : 9.279 159.045 604 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.49 % Allowed : 18.30 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.37), residues: 536 helix: 0.73 (0.31), residues: 295 sheet: -0.58 (0.70), residues: 43 loop : 0.59 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.012 0.001 TYR A 853 PHE 0.014 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4404) covalent geometry : angle 0.53449 ( 5961) hydrogen bonds : bond 0.04385 ( 200) hydrogen bonds : angle 5.51490 ( 567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.119 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 46 average time/residue: 0.4227 time to fit residues: 20.4317 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.1980 chunk 38 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061992 restraints weight = 12120.169| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.65 r_work: 0.3098 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4404 Z= 0.112 Angle : 0.498 8.528 5961 Z= 0.264 Chirality : 0.040 0.132 650 Planarity : 0.004 0.031 780 Dihedral : 8.968 155.485 603 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.27 % Allowed : 17.86 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.89 (0.37), residues: 536 helix: 0.93 (0.31), residues: 294 sheet: -0.63 (0.72), residues: 43 loop : 0.63 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.013 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4404) covalent geometry : angle 0.49755 ( 5961) hydrogen bonds : bond 0.03858 ( 200) hydrogen bonds : angle 5.33797 ( 567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.167 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 48 average time/residue: 0.4425 time to fit residues: 22.2578 Evaluate side-chains 37 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 26 optimal weight: 0.0770 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062462 restraints weight = 12109.772| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.67 r_work: 0.3112 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4404 Z= 0.107 Angle : 0.492 8.790 5961 Z= 0.261 Chirality : 0.040 0.129 650 Planarity : 0.003 0.030 780 Dihedral : 8.855 153.974 603 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.27 % Allowed : 17.43 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.94 (0.37), residues: 536 helix: 0.97 (0.32), residues: 295 sheet: -0.57 (0.74), residues: 43 loop : 0.63 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.013 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4404) covalent geometry : angle 0.49161 ( 5961) hydrogen bonds : bond 0.03690 ( 200) hydrogen bonds : angle 5.20584 ( 567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 48 average time/residue: 0.4110 time to fit residues: 20.8360 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0470 chunk 50 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 955 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062813 restraints weight = 12391.534| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.69 r_work: 0.3120 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4404 Z= 0.106 Angle : 0.500 9.999 5961 Z= 0.263 Chirality : 0.040 0.130 650 Planarity : 0.003 0.029 780 Dihedral : 8.775 152.563 603 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.92 % Allowed : 17.65 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.38), residues: 536 helix: 1.01 (0.32), residues: 294 sheet: -0.54 (0.76), residues: 43 loop : 0.65 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.012 0.001 TYR A 853 PHE 0.011 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.000 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4404) covalent geometry : angle 0.50018 ( 5961) hydrogen bonds : bond 0.03615 ( 200) hydrogen bonds : angle 5.19382 ( 567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 852 MET cc_start: 0.8717 (tpp) cc_final: 0.8399 (tpt) outliers start: 18 outliers final: 7 residues processed: 51 average time/residue: 0.4561 time to fit residues: 24.2965 Evaluate side-chains 39 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 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 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060674 restraints weight = 12334.971| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.64 r_work: 0.3065 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4404 Z= 0.166 Angle : 0.586 9.736 5961 Z= 0.307 Chirality : 0.043 0.152 650 Planarity : 0.004 0.032 780 Dihedral : 9.059 154.614 603 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.05 % Allowed : 18.74 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.37), residues: 536 helix: 0.92 (0.32), residues: 294 sheet: -0.58 (0.74), residues: 43 loop : 0.65 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.012 0.001 PHE A 879 TRP 0.004 0.001 TRP A 799 HIS 0.005 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4404) covalent geometry : angle 0.58613 ( 5961) hydrogen bonds : bond 0.04242 ( 200) hydrogen bonds : angle 5.35977 ( 567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.104 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 46 average time/residue: 0.4282 time to fit residues: 20.6248 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060681 restraints weight = 12355.089| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.65 r_work: 0.3064 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4404 Z= 0.159 Angle : 0.585 11.844 5961 Z= 0.304 Chirality : 0.043 0.149 650 Planarity : 0.004 0.033 780 Dihedral : 9.082 154.851 603 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.05 % Allowed : 19.39 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.37), residues: 536 helix: 0.88 (0.32), residues: 294 sheet: -0.56 (0.74), residues: 43 loop : 0.64 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.012 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4404) covalent geometry : angle 0.58504 ( 5961) hydrogen bonds : bond 0.04185 ( 200) hydrogen bonds : angle 5.38630 ( 567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 852 MET cc_start: 0.8723 (tpp) cc_final: 0.8451 (tpt) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.4171 time to fit residues: 19.8212 Evaluate side-chains 41 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061030 restraints weight = 12471.684| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.63 r_work: 0.3072 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4404 Z= 0.149 Angle : 0.581 10.741 5961 Z= 0.304 Chirality : 0.042 0.174 650 Planarity : 0.004 0.032 780 Dihedral : 9.058 154.672 603 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.83 % Allowed : 19.83 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.37), residues: 536 helix: 0.89 (0.32), residues: 295 sheet: -0.54 (0.74), residues: 43 loop : 0.65 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.012 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4404) covalent geometry : angle 0.58075 ( 5961) hydrogen bonds : bond 0.04106 ( 200) hydrogen bonds : angle 5.34744 ( 567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.299 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 44 average time/residue: 0.4007 time to fit residues: 18.7681 Evaluate side-chains 42 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061451 restraints weight = 12244.178| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.65 r_work: 0.3082 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4404 Z= 0.136 Angle : 0.574 11.786 5961 Z= 0.300 Chirality : 0.042 0.176 650 Planarity : 0.004 0.032 780 Dihedral : 8.994 153.874 603 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.40 % Allowed : 20.26 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.38), residues: 536 helix: 0.93 (0.32), residues: 295 sheet: -0.53 (0.74), residues: 43 loop : 0.67 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.011 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4404) covalent geometry : angle 0.57444 ( 5961) hydrogen bonds : bond 0.03945 ( 200) hydrogen bonds : angle 5.32109 ( 567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 852 MET cc_start: 0.8660 (tpp) cc_final: 0.8341 (tpt) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.4692 time to fit residues: 21.1255 Evaluate side-chains 40 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 968 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061041 restraints weight = 12294.873| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.62 r_work: 0.3075 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4404 Z= 0.151 Angle : 0.593 11.393 5961 Z= 0.310 Chirality : 0.043 0.192 650 Planarity : 0.004 0.032 780 Dihedral : 9.054 154.496 603 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.18 % Allowed : 20.70 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.89 (0.37), residues: 536 helix: 0.90 (0.32), residues: 295 sheet: -0.55 (0.74), residues: 43 loop : 0.65 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.011 0.001 TYR A 853 PHE 0.011 0.001 PHE A 879 TRP 0.004 0.001 TRP A 569 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4404) covalent geometry : angle 0.59350 ( 5961) hydrogen bonds : bond 0.04098 ( 200) hydrogen bonds : angle 5.34939 ( 567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.72 seconds wall clock time: 26 minutes 30.36 seconds (1590.36 seconds total)