Starting phenix.real_space_refine on Wed Jun 3 11:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.map" model { file = "/net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc0_70305/06_2026/9oc0_70305.cif" } resolution = 2.97 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= 0.012 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 Ca 1 9.91 5 P 4 5.49 5 S 27 5.16 5 C 2691 2.51 5 N 577 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3985 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 881 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 963 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 887 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 966 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 1.34, per 1000 atoms: 0.34 Number of scatterers: 3985 At special positions: 0 Unit cell: (66.36, 71.4, 65.52, 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) Ca 1 19.99 S 27 16.00 P 4 15.00 O 685 8.00 N 577 7.00 C 2691 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: 0.33 Conformation dependent library (CDL) restraints added in 160.7 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.603A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.641A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 655 removed outlier: 3.893A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.799A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.577A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.550A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.801A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 820 through 845 Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.603A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.641A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 655 removed outlier: 3.893A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.800A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.577A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.551A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.802A pdb=" N LYS D 629 " --> pdb=" O GLY D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 Processing helix chain 'D' and resid 820 through 845 288 hydrogen bonds defined for protein. 864 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: 0.51 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 583 1.33 - 1.45: 1086 1.45 - 1.57: 2320 1.57 - 1.69: 8 1.69 - 1.81: 52 Bond restraints: 4049 Sorted by residual: bond pdb=" N GLN A 556 " pdb=" CA GLN A 556 " ideal model delta sigma weight residual 1.461 1.494 -0.032 9.20e-03 1.18e+04 1.25e+01 bond pdb=" N GLN C 556 " pdb=" CA GLN C 556 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.20e+01 bond pdb=" N PHE C 558 " pdb=" CA PHE C 558 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.80e+00 bond pdb=" N GLN C 559 " pdb=" CA GLN C 559 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.74e+00 bond pdb=" N SER A 553 " pdb=" CA SER A 553 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.63e+00 ... (remaining 4044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 5260 0.91 - 1.82: 163 1.82 - 2.74: 54 2.74 - 3.65: 19 3.65 - 4.56: 6 Bond angle restraints: 5502 Sorted by residual: angle pdb=" CA GLN C 559 " pdb=" C GLN C 559 " pdb=" O GLN C 559 " ideal model delta sigma weight residual 121.47 117.91 3.56 1.15e+00 7.56e-01 9.61e+00 angle pdb=" CA PHE C 558 " pdb=" CB PHE C 558 " pdb=" CG PHE C 558 " ideal model delta sigma weight residual 113.80 116.86 -3.06 1.00e+00 1.00e+00 9.39e+00 angle pdb=" N MET C 555 " pdb=" CA MET C 555 " pdb=" C MET C 555 " ideal model delta sigma weight residual 113.16 109.89 3.27 1.24e+00 6.50e-01 6.97e+00 angle pdb=" N PHE A 554 " pdb=" CA PHE A 554 " pdb=" C PHE A 554 " ideal model delta sigma weight residual 113.20 110.03 3.17 1.21e+00 6.83e-01 6.87e+00 angle pdb=" CA CYS D 838 " pdb=" C CYS D 838 " pdb=" O CYS D 838 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.39e+00 ... (remaining 5497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2283 16.20 - 32.40: 92 32.40 - 48.60: 30 48.60 - 64.80: 17 64.80 - 81.00: 6 Dihedral angle restraints: 2428 sinusoidal: 960 harmonic: 1468 Sorted by residual: dihedral pdb=" CA ALA A 637 " pdb=" C ALA A 637 " pdb=" N GLY A 638 " pdb=" CA GLY A 638 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ALA C 637 " pdb=" C ALA C 637 " pdb=" N GLY C 638 " pdb=" CA GLY C 638 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA MET B 818 " pdb=" C MET B 818 " pdb=" N ALA B 819 " pdb=" CA ALA B 819 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 2425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 491 0.032 - 0.064: 139 0.064 - 0.096: 24 0.096 - 0.128: 6 0.128 - 0.160: 4 Chirality restraints: 664 Sorted by residual: chirality pdb=" CA PHE A 554 " pdb=" N PHE A 554 " pdb=" C PHE A 554 " pdb=" CB PHE A 554 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA PHE C 558 " pdb=" N PHE C 558 " pdb=" C PHE C 558 " pdb=" CB PHE C 558 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA MET C 555 " pdb=" N MET C 555 " pdb=" C MET C 555 " pdb=" CB MET C 555 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 661 not shown) Planarity restraints: 629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.52e-01 pdb=" N PRO B 553 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.42e-01 pdb=" N PRO D 553 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 623 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.16e-01 pdb=" N PRO C 624 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 624 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 624 " 0.011 5.00e-02 4.00e+02 ... (remaining 626 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1484 2.91 - 3.41: 4016 3.41 - 3.90: 6311 3.90 - 4.40: 7100 4.40 - 4.90: 12132 Nonbonded interactions: 31043 Sorted by model distance: nonbonded pdb=" O21 POV A 901 " pdb=" O31 POV A 901 " model vdw 2.409 2.432 nonbonded pdb=" O PHE C 554 " pdb=" OH TYR C 647 " model vdw 2.425 3.040 nonbonded pdb=" O21 POV C 902 " pdb=" O31 POV C 902 " model vdw 2.462 2.432 nonbonded pdb=" O LEU C 614 " pdb=" O HOH C1001 " model vdw 2.464 3.040 nonbonded pdb=" O21 POV C 901 " pdb=" O31 POV C 901 " model vdw 2.468 2.432 ... (remaining 31038 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 551 through 581 or (resid 582 and (name N or name CA or na \ me C or name O or name CB )) or resid 583 through 902)) } ncs_group { reference = (chain 'B' and resid 544 through 901) selection = (chain 'D' and (resid 544 through 630 or (resid 631 and (name N or name CA or na \ me C or name O or name CB )) or resid 632 through 901)) } 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: 5.570 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.050 Find NCS groups from input model: 0.080 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.002 0.034 4049 Z= 0.178 Angle : 0.466 4.562 5502 Z= 0.294 Chirality : 0.033 0.160 664 Planarity : 0.002 0.024 629 Dihedral : 11.863 80.999 1468 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.33), residues: 488 helix: 0.82 (0.23), residues: 368 sheet: None (None), residues: 0 loop : -2.00 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.004 0.001 TYR D 823 PHE 0.006 0.001 PHE C 639 TRP 0.006 0.001 TRP C 636 HIS 0.001 0.000 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.18 ( 4049) covalent geometry : angle 0.46612 / 0.29 ( 5502) hydrogen bonds : bond 0.26048 / 16.78 ( 288) hydrogen bonds : angle 6.20760 / 4.54 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.148 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 99 average time/residue: 0.2794 time to fit residues: 29.3487 Evaluate side-chains 78 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN B 812 GLN C 571 HIS D 615 ASN D 812 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145024 restraints weight = 4328.082| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.35 r_work: 0.3445 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4049 Z= 0.156 Angle : 0.542 5.988 5502 Z= 0.286 Chirality : 0.037 0.123 664 Planarity : 0.004 0.028 629 Dihedral : 13.885 82.424 815 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.34 % Allowed : 8.43 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.35), residues: 488 helix: 1.86 (0.24), residues: 378 sheet: None (None), residues: 0 loop : -1.90 (0.50), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.017 0.001 TYR C 578 PHE 0.013 0.002 PHE B 642 TRP 0.008 0.002 TRP B 607 HIS 0.003 0.002 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 4049) covalent geometry : angle 0.54227 / 0.29 ( 5502) hydrogen bonds : bond 0.05635 / 3.57 ( 288) hydrogen bonds : angle 3.95873 / 2.81 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.151 Fit side-chains REVERT: A 568 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (mt) REVERT: C 568 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (mt) REVERT: D 834 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7566 (mp) outliers start: 19 outliers final: 10 residues processed: 80 average time/residue: 0.2957 time to fit residues: 25.0541 Evaluate side-chains 78 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN B 616 ASN D 615 ASN D 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143598 restraints weight = 4379.356| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.65 r_work: 0.3491 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4049 Z= 0.116 Angle : 0.477 5.842 5502 Z= 0.250 Chirality : 0.035 0.114 664 Planarity : 0.003 0.025 629 Dihedral : 13.265 80.627 815 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.18 % Allowed : 9.55 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.37), residues: 488 helix: 2.12 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -2.28 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.021 0.001 TYR C 578 PHE 0.011 0.001 PHE B 642 TRP 0.007 0.001 TRP B 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 4049) covalent geometry : angle 0.47653 / 0.25 ( 5502) hydrogen bonds : bond 0.04490 / 2.85 ( 288) hydrogen bonds : angle 3.58446 / 2.57 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.185 Fit side-chains REVERT: A 568 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (mt) REVERT: B 615 ASN cc_start: 0.8171 (t0) cc_final: 0.7947 (t0) REVERT: C 568 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8077 (mt) REVERT: D 834 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7314 (mp) outliers start: 22 outliers final: 8 residues processed: 82 average time/residue: 0.3103 time to fit residues: 26.9406 Evaluate side-chains 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141764 restraints weight = 4264.721| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.33 r_work: 0.3418 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4049 Z= 0.152 Angle : 0.535 5.805 5502 Z= 0.276 Chirality : 0.037 0.157 664 Planarity : 0.003 0.026 629 Dihedral : 13.437 86.855 815 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 7.87 % Allowed : 9.27 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.36), residues: 488 helix: 2.11 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -2.05 (0.51), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.008 0.001 TYR A 578 PHE 0.014 0.001 PHE B 642 TRP 0.008 0.001 TRP B 635 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4049) covalent geometry : angle 0.53485 / 0.28 ( 5502) hydrogen bonds : bond 0.05073 / 3.20 ( 288) hydrogen bonds : angle 3.70209 / 2.64 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.140 Fit side-chains REVERT: A 568 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 819 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7326 (tt) REVERT: B 840 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.5835 (t-90) REVERT: C 568 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8325 (mt) REVERT: D 615 ASN cc_start: 0.8191 (t0) cc_final: 0.7977 (t0) REVERT: D 834 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7634 (mp) REVERT: D 840 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.5877 (t-90) outliers start: 28 outliers final: 10 residues processed: 78 average time/residue: 0.3251 time to fit residues: 26.7678 Evaluate side-chains 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140205 restraints weight = 4298.574| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.31 r_work: 0.3413 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4049 Z= 0.141 Angle : 0.540 8.798 5502 Z= 0.271 Chirality : 0.036 0.124 664 Planarity : 0.003 0.026 629 Dihedral : 13.227 89.686 815 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 8.15 % Allowed : 11.52 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.36), residues: 488 helix: 2.12 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -2.26 (0.50), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 582 TYR 0.010 0.001 TYR C 578 PHE 0.013 0.001 PHE D 642 TRP 0.010 0.001 TRP B 607 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4049) covalent geometry : angle 0.53982 / 0.27 ( 5502) hydrogen bonds : bond 0.04787 / 3.02 ( 288) hydrogen bonds : angle 3.61070 / 2.58 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.142 Fit side-chains REVERT: A 568 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 840 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5847 (t-90) REVERT: C 568 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8291 (mt) REVERT: D 615 ASN cc_start: 0.8168 (t0) cc_final: 0.7961 (t0) REVERT: D 834 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7607 (mp) REVERT: D 840 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5983 (t-90) outliers start: 29 outliers final: 11 residues processed: 82 average time/residue: 0.3208 time to fit residues: 27.7847 Evaluate side-chains 82 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.169289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143686 restraints weight = 4308.623| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.34 r_work: 0.3445 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4049 Z= 0.116 Angle : 0.505 8.639 5502 Z= 0.255 Chirality : 0.036 0.185 664 Planarity : 0.003 0.029 629 Dihedral : 12.693 89.106 815 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 7.30 % Allowed : 13.20 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.37), residues: 488 helix: 2.19 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -2.85 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 582 TYR 0.010 0.001 TYR C 578 PHE 0.011 0.001 PHE B 642 TRP 0.009 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 4049) covalent geometry : angle 0.50518 / 0.26 ( 5502) hydrogen bonds : bond 0.04246 / 2.70 ( 288) hydrogen bonds : angle 3.47442 / 2.48 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.113 Fit side-chains REVERT: A 568 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 819 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7266 (tt) REVERT: B 840 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.5874 (t-90) REVERT: C 568 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8264 (mt) REVERT: D 615 ASN cc_start: 0.8152 (t0) cc_final: 0.7915 (t0) REVERT: D 834 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7620 (mp) REVERT: D 840 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6066 (t-90) outliers start: 26 outliers final: 12 residues processed: 81 average time/residue: 0.3142 time to fit residues: 26.8253 Evaluate side-chains 83 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.167865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142275 restraints weight = 4315.759| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.32 r_work: 0.3411 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4049 Z= 0.125 Angle : 0.513 9.329 5502 Z= 0.260 Chirality : 0.037 0.187 664 Planarity : 0.003 0.029 629 Dihedral : 12.701 86.904 815 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.18 % Allowed : 14.04 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.88 (0.37), residues: 488 helix: 2.14 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -2.88 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.010 0.001 TYR A 578 PHE 0.012 0.001 PHE D 642 TRP 0.008 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4049) covalent geometry : angle 0.51288 / 0.26 ( 5502) hydrogen bonds : bond 0.04474 / 2.84 ( 288) hydrogen bonds : angle 3.49146 / 2.49 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.141 Fit side-chains REVERT: A 568 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8304 (mt) REVERT: A 576 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: A 819 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7280 (tt) REVERT: B 840 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.5924 (t-90) REVERT: C 568 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8285 (mt) REVERT: C 576 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: D 615 ASN cc_start: 0.8158 (t0) cc_final: 0.7917 (t0) REVERT: D 834 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7671 (mp) REVERT: D 840 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6048 (t-90) outliers start: 22 outliers final: 10 residues processed: 80 average time/residue: 0.3094 time to fit residues: 26.0983 Evaluate side-chains 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.169080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143576 restraints weight = 4245.427| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.32 r_work: 0.3421 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4049 Z= 0.118 Angle : 0.502 9.153 5502 Z= 0.255 Chirality : 0.036 0.199 664 Planarity : 0.003 0.030 629 Dihedral : 12.528 86.226 815 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.74 % Allowed : 13.76 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.37), residues: 488 helix: 2.23 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -2.94 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.008 0.001 TYR C 578 PHE 0.012 0.001 PHE D 642 TRP 0.008 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4049) covalent geometry : angle 0.50205 / 0.26 ( 5502) hydrogen bonds : bond 0.04272 / 2.72 ( 288) hydrogen bonds : angle 3.45701 / 2.47 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.132 Fit side-chains REVERT: A 568 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (mt) REVERT: A 576 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: B 840 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5939 (t-90) REVERT: C 568 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8279 (mt) REVERT: C 576 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8089 (mtm) REVERT: D 615 ASN cc_start: 0.8081 (t0) cc_final: 0.7837 (t0) REVERT: D 834 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7672 (mp) REVERT: D 840 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6053 (t-90) outliers start: 24 outliers final: 10 residues processed: 80 average time/residue: 0.3186 time to fit residues: 26.8802 Evaluate side-chains 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141279 restraints weight = 4355.599| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.35 r_work: 0.3427 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4049 Z= 0.137 Angle : 0.542 9.750 5502 Z= 0.272 Chirality : 0.038 0.224 664 Planarity : 0.003 0.030 629 Dihedral : 12.773 84.926 815 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.74 % Allowed : 14.04 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.37), residues: 488 helix: 2.07 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -2.91 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.010 0.001 TYR C 578 PHE 0.013 0.001 PHE D 642 TRP 0.008 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4049) covalent geometry : angle 0.54223 / 0.27 ( 5502) hydrogen bonds : bond 0.04716 / 2.99 ( 288) hydrogen bonds : angle 3.56032 / 2.53 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.140 Fit side-chains REVERT: A 568 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8333 (mt) REVERT: A 576 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8241 (mtm) REVERT: B 840 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: C 568 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (mt) REVERT: D 615 ASN cc_start: 0.8128 (t0) cc_final: 0.7862 (t0) REVERT: D 834 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7670 (mp) REVERT: D 840 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6073 (t-90) outliers start: 24 outliers final: 11 residues processed: 81 average time/residue: 0.3130 time to fit residues: 26.8034 Evaluate side-chains 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.167962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142208 restraints weight = 4278.667| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.35 r_work: 0.3416 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4049 Z= 0.139 Angle : 0.542 9.501 5502 Z= 0.274 Chirality : 0.038 0.223 664 Planarity : 0.003 0.030 629 Dihedral : 12.779 87.127 815 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.18 % Allowed : 14.61 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.37), residues: 488 helix: 2.11 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -3.11 (0.52), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.009 0.001 TYR C 578 PHE 0.013 0.001 PHE D 642 TRP 0.009 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4049) covalent geometry : angle 0.54175 / 0.27 ( 5502) hydrogen bonds : bond 0.04716 / 3.00 ( 288) hydrogen bonds : angle 3.57194 / 2.54 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.119 Fit side-chains REVERT: A 568 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (mt) REVERT: A 576 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (mtm) REVERT: A 819 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7230 (tt) REVERT: B 840 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.5907 (t-90) REVERT: C 568 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 615 ASN cc_start: 0.8150 (t0) cc_final: 0.7924 (t0) REVERT: D 834 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7642 (mp) REVERT: D 840 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.5974 (t-90) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.3130 time to fit residues: 27.3491 Evaluate side-chains 88 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 840 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.167419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141793 restraints weight = 4323.059| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.34 r_work: 0.3426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4049 Z= 0.128 Angle : 0.539 9.446 5502 Z= 0.271 Chirality : 0.038 0.220 664 Planarity : 0.003 0.030 629 Dihedral : 12.679 85.917 815 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.74 % Allowed : 14.33 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.37), residues: 488 helix: 2.19 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -3.13 (0.52), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.009 0.001 TYR C 578 PHE 0.012 0.001 PHE D 642 TRP 0.009 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4049) covalent geometry : angle 0.53858 / 0.27 ( 5502) hydrogen bonds : bond 0.04557 / 2.90 ( 288) hydrogen bonds : angle 3.53908 / 2.52 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.66 seconds wall clock time: 25 minutes 55.12 seconds (1555.12 seconds total)