Starting phenix.real_space_refine on Wed Jul 1 23:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc0_70305/07_2026/9oc0_70305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc0_70305/07_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_70305/07_2026/9oc0_70305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc0_70305/07_2026/9oc0_70305.map" model { file = "/net/cci-nas-00/data/ceres_data/9oc0_70305/07_2026/9oc0_70305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc0_70305/07_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-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 1.41, per 1000 atoms: 0.35 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: 0.47 Conformation dependent library (CDL) restraints added in 166.7 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: 0.05 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: 0.47 Time building geometry restraints manager: 0.58 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: 9.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.030 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.141 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 99 average time/residue: 0.2816 time to fit residues: 29.6214 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 : 0.137 ------------------------------------------------------------------------------- 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... 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 = 0.3844 r_free = 0.3844 target = 0.168277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142568 restraints weight = 4354.251| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.34 r_work: 0.3426 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4049 Z= 0.155 Angle : 0.546 6.025 5502 Z= 0.287 Chirality : 0.037 0.119 664 Planarity : 0.004 0.030 629 Dihedral : 13.929 82.590 815 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % 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: 1.61 (0.35), residues: 488 helix: 1.87 (0.24), residues: 378 sheet: None (None), residues: 0 loop : -1.86 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.018 0.002 TYR C 578 PHE 0.013 0.002 PHE B 642 TRP 0.008 0.002 TRP D 635 HIS 0.003 0.002 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4049) covalent geometry : angle 0.54578 / 0.29 ( 5502) hydrogen bonds : bond 0.05477 / 3.48 ( 288) hydrogen bonds : angle 3.95261 / 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 90 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.123 Fit side-chains REVERT: A 568 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8308 (mt) REVERT: C 568 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 834 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7608 (mp) outliers start: 19 outliers final: 10 residues processed: 81 average time/residue: 0.3198 time to fit residues: 27.4384 Evaluate side-chains 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3820 r_free = 0.3820 target = 0.165898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140280 restraints weight = 4318.583| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.32 r_work: 0.3403 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4049 Z= 0.164 Angle : 0.543 5.653 5502 Z= 0.284 Chirality : 0.037 0.120 664 Planarity : 0.004 0.026 629 Dihedral : 14.222 88.315 815 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.74 % Allowed : 8.15 % Favored : 85.11 % 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: 1.61 (0.35), residues: 488 helix: 1.88 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -2.06 (0.52), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.009 0.001 TYR A 578 PHE 0.014 0.002 PHE D 642 TRP 0.010 0.001 TRP D 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 4049) covalent geometry : angle 0.54304 / 0.28 ( 5502) hydrogen bonds : bond 0.05522 / 3.49 ( 288) hydrogen bonds : angle 3.83296 / 2.74 ( 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 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.132 Fit side-chains REVERT: A 568 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B 615 ASN cc_start: 0.8193 (t0) cc_final: 0.7986 (t0) REVERT: C 568 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 819 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7278 (tt) REVERT: D 834 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7596 (mp) outliers start: 24 outliers final: 6 residues processed: 78 average time/residue: 0.3189 time to fit residues: 26.3122 Evaluate side-chains 77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 821 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 819 LEU 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: 0.5980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144992 restraints weight = 4292.087| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.33 r_work: 0.3453 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4049 Z= 0.117 Angle : 0.499 6.220 5502 Z= 0.256 Chirality : 0.035 0.131 664 Planarity : 0.003 0.026 629 Dihedral : 13.305 88.294 815 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.90 % Allowed : 10.39 % Favored : 83.71 % 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: 2.08 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -2.56 (0.52), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.010 0.001 TYR A 578 PHE 0.010 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 0.00247 / 0.12 ( 4049) covalent geometry : angle 0.49945 / 0.26 ( 5502) hydrogen bonds : bond 0.04322 / 2.74 ( 288) hydrogen bonds : angle 3.57556 / 2.56 ( 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 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.143 Fit side-chains REVERT: A 568 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 615 ASN cc_start: 0.8123 (t0) cc_final: 0.7919 (t0) REVERT: B 817 ASN cc_start: 0.8054 (p0) cc_final: 0.7821 (p0) REVERT: B 840 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.5767 (t-90) REVERT: C 568 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8257 (mt) REVERT: C 819 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7262 (tt) REVERT: D 834 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7570 (mp) outliers start: 21 outliers final: 8 residues processed: 76 average time/residue: 0.3526 time to fit residues: 28.1676 Evaluate side-chains 77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 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 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 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 819 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 0.0070 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148065 restraints weight = 4291.206| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.19 r_work: 0.3485 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4049 Z= 0.111 Angle : 0.489 7.268 5502 Z= 0.249 Chirality : 0.035 0.146 664 Planarity : 0.003 0.026 629 Dihedral : 12.735 89.550 815 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.18 % Allowed : 12.92 % Favored : 80.90 % 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: 2.07 (0.37), residues: 488 helix: 2.22 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -2.54 (0.52), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.010 0.001 TYR C 578 PHE 0.011 0.001 PHE D 642 TRP 0.008 0.001 TRP D 607 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 4049) covalent geometry : angle 0.48898 / 0.25 ( 5502) hydrogen bonds : bond 0.04111 / 2.60 ( 288) hydrogen bonds : angle 3.45596 / 2.49 ( 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 90 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.159 Fit side-chains REVERT: A 568 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 817 ASN cc_start: 0.8050 (p0) cc_final: 0.7777 (p0) REVERT: B 833 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6977 (tp) REVERT: B 840 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5838 (t-90) REVERT: C 568 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8197 (mt) REVERT: D 834 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7570 (mp) outliers start: 22 outliers final: 8 residues processed: 79 average time/residue: 0.2825 time to fit residues: 23.5956 Evaluate side-chains 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 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 575 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140260 restraints weight = 4309.430| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.34 r_work: 0.3397 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2966 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= 0.144 Angle : 0.524 5.858 5502 Z= 0.270 Chirality : 0.037 0.176 664 Planarity : 0.003 0.026 629 Dihedral : 13.074 86.402 815 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 7.02 % Allowed : 12.08 % Favored : 80.90 % 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: 2.17 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -2.33 (0.50), residues: 106 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 0.008 0.001 TRP D 607 HIS 0.001 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4049) covalent geometry : angle 0.52367 / 0.27 ( 5502) hydrogen bonds : bond 0.04844 / 3.07 ( 288) hydrogen bonds : angle 3.60510 / 2.57 ( 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 92 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.142 Fit side-chains REVERT: A 568 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 576 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: B 615 ASN cc_start: 0.8179 (t0) cc_final: 0.7954 (t0) REVERT: B 817 ASN cc_start: 0.8117 (p0) cc_final: 0.7852 (p0) REVERT: B 840 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.5893 (t-90) REVERT: C 568 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8334 (mt) REVERT: C 576 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8346 (mtm) REVERT: D 834 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7650 (mp) REVERT: D 840 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.5959 (t-90) outliers start: 25 outliers final: 10 residues processed: 81 average time/residue: 0.2937 time to fit residues: 25.1744 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 575 VAL 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 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: 0.7980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140492 restraints weight = 4319.303| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.34 r_work: 0.3386 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3038 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= 0.147 Angle : 0.536 7.732 5502 Z= 0.274 Chirality : 0.038 0.213 664 Planarity : 0.003 0.026 629 Dihedral : 13.067 90.949 815 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 7.02 % Allowed : 12.64 % 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: 1.68 (0.37), residues: 488 helix: 2.00 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -2.92 (0.52), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 630 TYR 0.011 0.001 TYR A 578 PHE 0.013 0.001 PHE D 642 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4049) covalent geometry : angle 0.53648 / 0.27 ( 5502) hydrogen bonds : bond 0.04862 / 3.08 ( 288) hydrogen bonds : angle 3.61935 / 2.58 ( 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 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.151 Fit side-chains REVERT: A 568 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 615 ASN cc_start: 0.8244 (t0) cc_final: 0.8028 (t0) REVERT: B 817 ASN cc_start: 0.8071 (p0) cc_final: 0.7793 (p0) REVERT: B 840 HIS cc_start: 0.6528 (OUTLIER) cc_final: 0.5826 (t-90) REVERT: C 568 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 576 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: D 615 ASN cc_start: 0.8209 (t0) cc_final: 0.8000 (t0) REVERT: D 834 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7522 (mp) REVERT: D 840 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.6036 (t-90) outliers start: 25 outliers final: 13 residues processed: 82 average time/residue: 0.2920 time to fit residues: 25.3273 Evaluate side-chains 87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 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 831 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 576 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER 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: 0.8980 chunk 42 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 40 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.150123 restraints weight = 4242.711| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.23 r_work: 0.3461 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4049 Z= 0.113 Angle : 0.494 6.180 5502 Z= 0.253 Chirality : 0.037 0.217 664 Planarity : 0.003 0.026 629 Dihedral : 12.555 87.242 815 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.34 % Allowed : 14.61 % Favored : 80.06 % 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: 2.18 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -2.79 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 582 TYR 0.010 0.001 TYR C 578 PHE 0.011 0.001 PHE D 642 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 4049) covalent geometry : angle 0.49360 / 0.25 ( 5502) hydrogen bonds : bond 0.04163 / 2.66 ( 288) hydrogen bonds : angle 3.45809 / 2.48 ( 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 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.142 Fit side-chains REVERT: A 568 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 817 ASN cc_start: 0.8024 (p0) cc_final: 0.7721 (p0) REVERT: B 840 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.5911 (t-90) REVERT: C 568 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8223 (mt) REVERT: D 834 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7620 (mp) REVERT: D 840 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6060 (t-90) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 0.3257 time to fit residues: 26.4960 Evaluate side-chains 81 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 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 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: 0.5980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140722 restraints weight = 4375.309| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.35 r_work: 0.3400 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3117 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= 0.145 Angle : 0.537 6.068 5502 Z= 0.276 Chirality : 0.038 0.211 664 Planarity : 0.003 0.027 629 Dihedral : 12.852 85.391 815 Min Nonbonded Distance : 2.333 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: 1.71 (0.37), residues: 488 helix: 1.99 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -2.87 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 630 TYR 0.009 0.001 TYR A 578 PHE 0.013 0.001 PHE B 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 0.00328 / 0.14 ( 4049) covalent geometry : angle 0.53706 / 0.28 ( 5502) hydrogen bonds : bond 0.04820 / 3.07 ( 288) hydrogen bonds : angle 3.57835 / 2.55 ( 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 89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.137 Fit side-chains REVERT: A 568 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 615 ASN cc_start: 0.8100 (t0) cc_final: 0.7888 (t0) REVERT: B 840 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.5890 (t-90) REVERT: C 568 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 819 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7293 (tt) REVERT: D 834 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7665 (mp) REVERT: D 840 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.6040 (t-90) outliers start: 22 outliers final: 13 residues processed: 82 average time/residue: 0.3187 time to fit residues: 27.6283 Evaluate side-chains 86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 831 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 605 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 819 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.167583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142022 restraints weight = 4281.004| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.33 r_work: 0.3479 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4049 Z= 0.128 Angle : 0.526 5.972 5502 Z= 0.270 Chirality : 0.038 0.214 664 Planarity : 0.003 0.028 629 Dihedral : 12.718 85.909 815 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.62 % Allowed : 15.17 % 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: 1.77 (0.37), residues: 488 helix: 2.05 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -2.94 (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 0.012 0.001 PHE D 642 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 4049) covalent geometry : angle 0.52623 / 0.27 ( 5502) hydrogen bonds : bond 0.04571 / 2.92 ( 288) hydrogen bonds : angle 3.54397 / 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 88 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.141 Fit side-chains REVERT: A 568 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 840 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.5914 (t-90) REVERT: C 555 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7816 (mtt) REVERT: C 568 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 819 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7327 (tt) REVERT: D 834 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7629 (mp) REVERT: D 840 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.6081 (t-90) outliers start: 20 outliers final: 11 residues processed: 82 average time/residue: 0.2903 time to fit residues: 25.2017 Evaluate side-chains 86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 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 816 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 555 MET 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 605 SER Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 819 LEU 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: 0.9980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 ASN D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140970 restraints weight = 4325.934| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.34 r_work: 0.3392 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3181 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= 0.147 Angle : 0.559 7.218 5502 Z= 0.285 Chirality : 0.039 0.238 664 Planarity : 0.004 0.028 629 Dihedral : 12.915 87.655 815 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.18 % Allowed : 14.89 % 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: 1.58 (0.37), residues: 488 helix: 1.91 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -2.99 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.009 0.001 TYR C 578 PHE 0.013 0.001 PHE D 642 TRP 0.008 0.001 TRP D 607 HIS 0.002 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 4049) covalent geometry : angle 0.55919 / 0.29 ( 5502) hydrogen bonds : bond 0.04943 / 3.16 ( 288) hydrogen bonds : angle 3.62716 / 2.59 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.14 seconds wall clock time: 25 minutes 46.13 seconds (1546.13 seconds total)