Starting phenix.real_space_refine on Wed Jun 3 11:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.map" model { file = "/net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oc1_70306/06_2026/9oc1_70306.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 29 5.16 5 C 2718 2.51 5 N 574 2.21 5 O 705 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: 4031 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 905 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 959 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 905 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 961 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {' CA': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 1.17, per 1000 atoms: 0.29 Number of scatterers: 4031 At special positions: 0 Unit cell: (71.4, 76.44, 68.04, 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 29 16.00 P 4 15.00 O 705 8.00 N 574 7.00 C 2718 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: 0.38 Conformation dependent library (CDL) restraints added in 118.1 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: 16 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.501A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.540A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.558A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.785A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.501A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.504A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.692A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.609A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.501A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 3.539A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.559A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.786A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.501A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 removed outlier: 3.504A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.691A pdb=" N LYS D 629 " --> pdb=" O GLY D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 3.609A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 870 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: 0.49 Time building geometry restraints manager: 0.47 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: 587 1.33 - 1.45: 1100 1.45 - 1.57: 2333 1.57 - 1.69: 8 1.69 - 1.81: 56 Bond restraints: 4084 Sorted by residual: bond pdb=" N GLN A 559 " pdb=" CA GLN A 559 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.49e+00 bond pdb=" N PHE A 558 " pdb=" CA PHE A 558 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.07e+00 bond pdb=" N PHE C 558 " pdb=" CA PHE C 558 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.62e+00 bond pdb=" N LEU C 819 " pdb=" CA LEU C 819 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.01e+00 bond pdb=" N GLN C 556 " pdb=" CA GLN C 556 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.88e+00 ... (remaining 4079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 5311 0.94 - 1.88: 163 1.88 - 2.83: 42 2.83 - 3.77: 24 3.77 - 4.71: 4 Bond angle restraints: 5544 Sorted by residual: angle pdb=" C LEU D 551 " pdb=" N GLU D 552 " pdb=" CA GLU D 552 " ideal model delta sigma weight residual 120.26 124.80 -4.54 1.34e+00 5.57e-01 1.15e+01 angle pdb=" C LEU B 551 " pdb=" N GLU B 552 " pdb=" CA GLU B 552 " ideal model delta sigma weight residual 120.26 124.77 -4.51 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA PHE C 558 " pdb=" CB PHE C 558 " pdb=" CG PHE C 558 " ideal model delta sigma weight residual 113.80 117.01 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CA GLN A 559 " pdb=" C GLN A 559 " pdb=" O GLN A 559 " ideal model delta sigma weight residual 121.72 118.06 3.66 1.18e+00 7.18e-01 9.64e+00 angle pdb=" CA PHE A 558 " pdb=" CB PHE A 558 " pdb=" CG PHE A 558 " ideal model delta sigma weight residual 113.80 116.72 -2.92 1.00e+00 1.00e+00 8.54e+00 ... (remaining 5539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 2379 29.20 - 58.40: 58 58.40 - 87.59: 7 87.59 - 116.79: 2 116.79 - 145.99: 4 Dihedral angle restraints: 2450 sinusoidal: 982 harmonic: 1468 Sorted by residual: dihedral pdb=" C29 POV A 902 " pdb="C210 POV A 902 " pdb="C211 POV A 902 " pdb="C212 POV A 902 " ideal model delta sinusoidal sigma weight residual 112.25 -101.76 -145.99 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3 POV C 901 " pdb=" C31 POV C 901 " pdb=" O31 POV C 901 " pdb=" C32 POV C 901 " ideal model delta sinusoidal sigma weight residual 172.61 -47.57 -139.82 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C29 POV C 901 " pdb="C210 POV C 901 " pdb="C211 POV C 901 " pdb="C212 POV C 901 " ideal model delta sinusoidal sigma weight residual 112.25 -108.76 -138.99 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 2447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 479 0.030 - 0.059: 141 0.059 - 0.089: 32 0.089 - 0.119: 6 0.119 - 0.148: 8 Chirality restraints: 666 Sorted by residual: chirality pdb=" CA LEU A 819 " pdb=" N LEU A 819 " pdb=" C LEU A 819 " pdb=" CB LEU A 819 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA LEU C 819 " pdb=" N LEU C 819 " pdb=" C LEU C 819 " pdb=" CB LEU C 819 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-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 2.65 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 663 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 546 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.92e-01 pdb=" N PRO D 547 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 546 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.90e-01 pdb=" N PRO B 547 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.85e-01 pdb=" N PRO B 553 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " -0.013 5.00e-02 4.00e+02 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1174 2.82 - 3.34: 3930 3.34 - 3.86: 6281 3.86 - 4.38: 7585 4.38 - 4.90: 12937 Nonbonded interactions: 31907 Sorted by model distance: nonbonded pdb=" O HOH C1001 " pdb=" O HOH D1004 " model vdw 2.298 3.040 nonbonded pdb=" O HOH A1001 " pdb=" O HOH B1004 " model vdw 2.306 3.040 nonbonded pdb=" O HOH B1010 " pdb=" O HOH B1012 " model vdw 2.344 3.040 nonbonded pdb=" O HOH C1007 " pdb=" O HOH D1009 " model vdw 2.344 3.040 nonbonded pdb=" O21 POV C 902 " pdb=" O31 POV C 902 " model vdw 2.365 2.432 ... (remaining 31902 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' and (resid 550 through 838 or resid 902)) selection = (chain 'C' and (resid 550 through 838 or resid 902)) } ncs_group { reference = (chain 'B' and (resid 545 through 809 or (resid 810 and (name N or name CA or na \ me C or name O or name CB )) or resid 811 through 901)) selection = (chain 'D' and (resid 545 through 657 or (resid 809 through 810 and (name N or n \ ame CA or name C or name O or name CB )) or resid 811 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: 7.140 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 5.730 Find NCS groups from input model: 0.090 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:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 0.035 4084 Z= 0.174 Angle : 0.471 4.711 5544 Z= 0.309 Chirality : 0.033 0.148 666 Planarity : 0.003 0.024 632 Dihedral : 14.249 145.988 1490 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.36 (0.33), residues: 488 helix: 0.92 (0.23), residues: 376 sheet: None (None), residues: 0 loop : -1.98 (0.46), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR A 647 PHE 0.007 0.001 PHE D 614 TRP 0.003 0.000 TRP A 608 HIS 0.001 0.000 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.17 ( 4084) covalent geometry : angle 0.47090 / 0.31 ( 5544) hydrogen bonds : bond 0.26088 / 17.50 ( 290) hydrogen bonds : angle 5.90089 / 4.18 ( 870) *********************** 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 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3624 time to fit residues: 31.9218 Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.147865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123718 restraints weight = 4716.004| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.61 r_work: 0.3275 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4084 Z= 0.138 Angle : 0.484 4.630 5544 Z= 0.263 Chirality : 0.035 0.121 666 Planarity : 0.004 0.030 632 Dihedral : 16.268 130.887 812 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.91 % Allowed : 5.74 % Favored : 92.35 % 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 (0.35), residues: 488 helix: 1.89 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.81 (0.54), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.009 0.001 TYR C 578 PHE 0.015 0.002 PHE C 627 TRP 0.007 0.001 TRP D 635 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 4084) covalent geometry : angle 0.48375 / 0.26 ( 5544) hydrogen bonds : bond 0.05799 / 3.73 ( 290) hydrogen bonds : angle 3.40428 / 2.47 ( 870) *********************** 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 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.140 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.4688 time to fit residues: 35.5143 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain D residue 601 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 817 ASN D 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125091 restraints weight = 4640.379| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.58 r_work: 0.3297 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4084 Z= 0.111 Angle : 0.420 4.664 5544 Z= 0.226 Chirality : 0.033 0.115 666 Planarity : 0.003 0.027 632 Dihedral : 15.534 127.486 812 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 8.47 % Favored : 88.80 % 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: 2.50 (0.37), residues: 488 helix: 2.36 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.74 (0.53), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.003 0.001 TYR C 578 PHE 0.014 0.001 PHE C 627 TRP 0.005 0.001 TRP B 635 HIS 0.001 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4084) covalent geometry : angle 0.41982 / 0.23 ( 5544) hydrogen bonds : bond 0.04981 / 3.22 ( 290) hydrogen bonds : angle 3.11620 / 2.26 ( 870) *********************** 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 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.144 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.4644 time to fit residues: 31.8612 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 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 817 ASN D 615 ASN D 817 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125424 restraints weight = 4607.284| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.48 r_work: 0.3286 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4084 Z= 0.147 Angle : 0.475 4.747 5544 Z= 0.252 Chirality : 0.035 0.122 666 Planarity : 0.004 0.027 632 Dihedral : 15.661 129.814 812 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.55 % Allowed : 9.02 % Favored : 87.43 % 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: 2.25 (0.37), residues: 488 helix: 2.17 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.72 (0.54), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 630 TYR 0.005 0.001 TYR C 578 PHE 0.014 0.002 PHE D 642 TRP 0.006 0.001 TRP B 610 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4084) covalent geometry : angle 0.47530 / 0.25 ( 5544) hydrogen bonds : bond 0.05836 / 3.78 ( 290) hydrogen bonds : angle 3.21560 / 2.33 ( 870) *********************** 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 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.102 Fit side-chains REVERT: A 564 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 564 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8250 (mp) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.4594 time to fit residues: 31.5310 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR 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 10 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.146107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123239 restraints weight = 4637.075| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.54 r_work: 0.3160 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4084 Z= 0.167 Angle : 0.503 4.729 5544 Z= 0.266 Chirality : 0.035 0.125 666 Planarity : 0.004 0.028 632 Dihedral : 15.963 133.592 812 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.55 % Allowed : 10.66 % Favored : 85.79 % 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: 1.83 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.44 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.006 0.001 TYR A 578 PHE 0.015 0.002 PHE B 642 TRP 0.006 0.001 TRP D 635 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 4084) covalent geometry : angle 0.50294 / 0.27 ( 5544) hydrogen bonds : bond 0.06181 / 4.00 ( 290) hydrogen bonds : angle 3.27773 / 2.38 ( 870) *********************** 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 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.091 Fit side-chains REVERT: A 556 GLN cc_start: 0.8639 (tp40) cc_final: 0.8433 (tp-100) REVERT: A 564 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8237 (mp) REVERT: C 564 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8207 (mp) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.4772 time to fit residues: 32.6850 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.143629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120027 restraints weight = 4720.808| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.56 r_work: 0.3177 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4084 Z= 0.134 Angle : 0.454 4.754 5544 Z= 0.243 Chirality : 0.034 0.119 666 Planarity : 0.004 0.026 632 Dihedral : 15.588 131.470 812 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 10.66 % Favored : 85.52 % 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: 2.17 (0.37), residues: 488 helix: 1.97 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.46 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR A 578 PHE 0.012 0.002 PHE B 642 TRP 0.006 0.001 TRP D 607 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4084) covalent geometry : angle 0.45381 / 0.24 ( 5544) hydrogen bonds : bond 0.05473 / 3.54 ( 290) hydrogen bonds : angle 3.19177 / 2.33 ( 870) *********************** 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 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.164 Fit side-chains REVERT: A 556 GLN cc_start: 0.8657 (tp40) cc_final: 0.8447 (tp-100) REVERT: A 564 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 564 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8263 (mp) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.4972 time to fit residues: 33.0206 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.151511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128160 restraints weight = 4644.260| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.57 r_work: 0.3325 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4084 Z= 0.111 Angle : 0.421 4.760 5544 Z= 0.226 Chirality : 0.033 0.117 666 Planarity : 0.003 0.027 632 Dihedral : 15.108 126.514 812 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 11.20 % Favored : 84.97 % 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: 2.46 (0.37), residues: 488 helix: 2.31 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.61 (0.53), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.003 0.001 TYR A 578 PHE 0.011 0.001 PHE A 627 TRP 0.005 0.001 TRP B 607 HIS 0.001 0.000 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 4084) covalent geometry : angle 0.42063 / 0.23 ( 5544) hydrogen bonds : bond 0.04781 / 3.09 ( 290) hydrogen bonds : angle 3.08747 / 2.26 ( 870) *********************** 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 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.141 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.4303 time to fit residues: 29.9891 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.142452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118973 restraints weight = 4663.091| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.54 r_work: 0.3252 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4084 Z= 0.151 Angle : 0.481 4.820 5544 Z= 0.257 Chirality : 0.035 0.124 666 Planarity : 0.004 0.027 632 Dihedral : 14.974 126.934 812 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.55 % Allowed : 11.48 % Favored : 84.97 % 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: 2.05 (0.37), residues: 488 helix: 1.87 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.41 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.005 0.001 TYR C 578 PHE 0.014 0.002 PHE B 642 TRP 0.006 0.001 TRP D 635 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4084) covalent geometry : angle 0.48148 / 0.26 ( 5544) hydrogen bonds : bond 0.05854 / 3.79 ( 290) hydrogen bonds : angle 3.28313 / 2.40 ( 870) *********************** 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 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.158 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.4564 time to fit residues: 29.3846 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.151193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127105 restraints weight = 4662.577| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.59 r_work: 0.3271 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4084 Z= 0.119 Angle : 0.433 4.775 5544 Z= 0.235 Chirality : 0.033 0.118 666 Planarity : 0.003 0.027 632 Dihedral : 14.478 122.428 812 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.01 % Allowed : 12.30 % Favored : 84.70 % 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: 2.25 (0.37), residues: 488 helix: 2.03 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.47 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.003 0.001 TYR C 578 PHE 0.011 0.001 PHE A 627 TRP 0.005 0.001 TRP D 635 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4084) covalent geometry : angle 0.43253 / 0.23 ( 5544) hydrogen bonds : bond 0.05054 / 3.28 ( 290) hydrogen bonds : angle 3.13115 / 2.29 ( 870) *********************** 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 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.124 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.4764 time to fit residues: 31.1574 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.143166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118922 restraints weight = 4646.366| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.60 r_work: 0.3227 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4084 Z= 0.149 Angle : 0.474 4.846 5544 Z= 0.255 Chirality : 0.035 0.122 666 Planarity : 0.004 0.027 632 Dihedral : 14.607 122.596 812 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.28 % Allowed : 12.30 % Favored : 84.43 % 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: 2.04 (0.37), residues: 488 helix: 1.88 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -1.47 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.005 0.001 TYR A 578 PHE 0.014 0.002 PHE D 642 TRP 0.006 0.001 TRP D 635 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4084) covalent geometry : angle 0.47431 / 0.26 ( 5544) hydrogen bonds : bond 0.05711 / 3.71 ( 290) hydrogen bonds : angle 3.21638 / 2.36 ( 870) ********************** 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 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.177 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 61 average time/residue: 0.4686 time to fit residues: 29.6614 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 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 = 0.3612 r_free = 0.3612 target = 0.143623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119520 restraints weight = 4653.570| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.59 r_work: 0.3220 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4084 Z= 0.144 Angle : 0.468 4.798 5544 Z= 0.253 Chirality : 0.034 0.121 666 Planarity : 0.004 0.027 632 Dihedral : 14.575 122.112 812 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 11.48 % Favored : 84.70 % 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: 2.01 (0.37), residues: 488 helix: 1.90 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -1.66 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.006 0.001 TYR D 823 PHE 0.013 0.002 PHE D 642 TRP 0.005 0.001 TRP D 607 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4084) covalent geometry : angle 0.46831 / 0.25 ( 5544) hydrogen bonds : bond 0.05643 / 3.66 ( 290) hydrogen bonds : angle 3.21088 / 2.36 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.05 seconds wall clock time: 27 minutes 56.64 seconds (1676.64 seconds total)