Starting phenix.real_space_refine on Tue May 13 16:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.map" model { file = "/net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp9_29360/05_2025/8fp9_29360.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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 S 76 5.16 5 Cl 4 4.86 5 C 7002 2.51 5 N 1708 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10851 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 9.17, per 1000 atoms: 0.85 Number of scatterers: 10851 At special positions: 0 Unit cell: (113.911, 113.911, 91.784, 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 Cl 4 17.00 S 76 16.00 O 2060 8.00 N 1708 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 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: 2.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 73.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 618 Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 826 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 618 Processing helix chain 'D' and resid 619 through 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.709A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.508A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.521A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.794A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.691A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.673A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.591A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.529A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.596A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.572A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.529A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA3, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 864 hydrogen bonds defined for protein. 2510 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: 3.19 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3226 1.34 - 1.46: 2541 1.46 - 1.58: 5041 1.58 - 1.70: 0 1.70 - 1.81: 116 Bond restraints: 10924 Sorted by residual: bond pdb=" CG GLU G 191 " pdb=" CD GLU G 191 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.51e-01 bond pdb=" CG GLU E 191 " pdb=" CD GLU E 191 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.44e-01 bond pdb=" N ASN B 619 " pdb=" CA ASN B 619 " ideal model delta sigma weight residual 1.458 1.468 -0.010 1.44e-02 4.82e+03 4.90e-01 bond pdb=" CB PRO B 520 " pdb=" CG PRO B 520 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.84e-01 bond pdb=" CB PRO D 520 " pdb=" CG PRO D 520 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.81e-01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 14441 1.13 - 2.27: 292 2.27 - 3.40: 42 3.40 - 4.53: 17 4.53 - 5.67: 6 Bond angle restraints: 14798 Sorted by residual: angle pdb=" N ASP D 519 " pdb=" CA ASP D 519 " pdb=" C ASP D 519 " ideal model delta sigma weight residual 109.81 115.48 -5.67 2.21e+00 2.05e-01 6.57e+00 angle pdb=" N ASP B 519 " pdb=" CA ASP B 519 " pdb=" C ASP B 519 " ideal model delta sigma weight residual 109.81 115.46 -5.65 2.21e+00 2.05e-01 6.54e+00 angle pdb=" N ASP E 88 " pdb=" CA ASP E 88 " pdb=" CB ASP E 88 " ideal model delta sigma weight residual 113.65 110.10 3.55 1.47e+00 4.63e-01 5.82e+00 angle pdb=" CA ASP B 519 " pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 118.44 122.10 -3.66 1.59e+00 3.96e-01 5.31e+00 angle pdb=" CA ASP D 519 " pdb=" C ASP D 519 " pdb=" N PRO D 520 " ideal model delta sigma weight residual 118.44 122.10 -3.66 1.59e+00 3.96e-01 5.30e+00 ... (remaining 14793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5403 17.89 - 35.79: 619 35.79 - 53.68: 168 53.68 - 71.58: 26 71.58 - 89.47: 16 Dihedral angle restraints: 6232 sinusoidal: 2298 harmonic: 3934 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -120.87 34.87 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA ALA E 87 " pdb=" C ALA E 87 " pdb=" N ASP E 88 " pdb=" CA ASP E 88 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1105 0.028 - 0.056: 338 0.056 - 0.085: 188 0.085 - 0.113: 37 0.113 - 0.141: 6 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL H 57 " pdb=" N VAL H 57 " pdb=" C VAL H 57 " pdb=" CB VAL H 57 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1671 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 107 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO H 108 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 108 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 107 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO F 108 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 108 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 108 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 519 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 520 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 520 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 520 " 0.016 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 726 2.74 - 3.28: 10800 3.28 - 3.82: 20325 3.82 - 4.36: 21626 4.36 - 4.90: 37809 Nonbonded interactions: 91286 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 179 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR E 30 " pdb=" OG SER E 179 " model vdw 2.200 3.040 nonbonded pdb=" NE2 GLN D 586 " pdb=" O HOH D 901 " model vdw 2.221 3.120 nonbonded pdb=" O HOH B1001 " pdb=" O HOH B1008 " model vdw 2.228 3.040 nonbonded pdb=" OG SER C 564 " pdb=" N SER C 565 " model vdw 2.229 3.120 ... (remaining 91281 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 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'B' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 through 552 or resid 564 through 588 or resid 590 thro \ ugh 614 or resid 616 through 826)) selection = (chain 'D' and (resid 511 through 588 or resid 590 through 614 or resid 616 thro \ ugh 626 or resid 784 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214 or resid 401)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 214 or resid 401)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 214 or resid 401)) } 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=0.50 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: 2.290 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.100 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.003 0.035 10932 Z= 0.126 Angle : 0.427 5.666 14814 Z= 0.242 Chirality : 0.036 0.141 1674 Planarity : 0.003 0.030 1808 Dihedral : 16.651 89.473 3688 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.98 % Allowed : 19.68 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.23), residues: 1336 helix: 4.00 (0.16), residues: 950 sheet: 0.37 (0.78), residues: 48 loop : -0.27 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 33 HIS 0.004 0.001 HIS H 205 PHE 0.010 0.001 PHE F 107 TYR 0.014 0.001 TYR G 89 ARG 0.005 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.12066 ( 864) hydrogen bonds : angle 4.12499 ( 2510) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.34502 ( 16) covalent geometry : bond 0.00255 (10924) covalent geometry : angle 0.42701 (14798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.052 Fit side-chains REVERT: D 629 MET cc_start: 0.6605 (tpt) cc_final: 0.6293 (tpp) REVERT: G 10 MET cc_start: 0.7887 (mmm) cc_final: 0.7662 (mmm) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 1.2072 time to fit residues: 190.5507 Evaluate side-chains 144 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 ASN D 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.190848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128152 restraints weight = 30800.580| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.60 r_work: 0.2914 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10932 Z= 0.167 Angle : 0.471 6.421 14814 Z= 0.265 Chirality : 0.038 0.129 1674 Planarity : 0.003 0.032 1808 Dihedral : 4.283 33.234 1479 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.04 % Allowed : 17.71 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.23), residues: 1336 helix: 3.95 (0.16), residues: 952 sheet: 0.20 (0.74), residues: 48 loop : -0.33 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 33 HIS 0.003 0.001 HIS H 205 PHE 0.012 0.002 PHE G 107 TYR 0.011 0.002 TYR G 89 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05949 ( 864) hydrogen bonds : angle 3.49418 ( 2510) SS BOND : bond 0.00231 ( 8) SS BOND : angle 0.36933 ( 16) covalent geometry : bond 0.00358 (10924) covalent geometry : angle 0.47116 (14798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.073 Fit side-chains REVERT: D 586 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: D 629 MET cc_start: 0.6427 (tpt) cc_final: 0.6225 (tpp) REVERT: E 31 ASP cc_start: 0.8340 (m-30) cc_final: 0.8134 (m-30) REVERT: E 204 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6618 (mtt180) REVERT: G 74 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6256 (ttpt) REVERT: G 204 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6617 (mtt90) REVERT: G 207 GLN cc_start: 0.6068 (tt0) cc_final: 0.5837 (tm-30) REVERT: F 69 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6446 (pt) REVERT: F 126 GLU cc_start: 0.5199 (OUTLIER) cc_final: 0.4726 (tm-30) REVERT: H 65 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6801 (ptm-80) outliers start: 34 outliers final: 12 residues processed: 169 average time/residue: 1.1202 time to fit residues: 205.1795 Evaluate side-chains 162 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 65 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131041 restraints weight = 34862.239| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.65 r_work: 0.2966 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10932 Z= 0.108 Angle : 0.400 6.731 14814 Z= 0.223 Chirality : 0.035 0.141 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.715 26.977 1474 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.33 % Allowed : 18.16 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.23), residues: 1336 helix: 4.18 (0.16), residues: 956 sheet: 0.78 (1.02), residues: 28 loop : -0.23 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 PHE 0.009 0.001 PHE G 107 TYR 0.011 0.001 TYR G 89 ARG 0.004 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 864) hydrogen bonds : angle 3.19491 ( 2510) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.38350 ( 16) covalent geometry : bond 0.00201 (10924) covalent geometry : angle 0.39956 (14798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.060 Fit side-chains REVERT: E 31 ASP cc_start: 0.8236 (m-30) cc_final: 0.7897 (m-30) REVERT: G 65 ARG cc_start: 0.7820 (ptm-80) cc_final: 0.7596 (ptm160) REVERT: G 74 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6226 (ttpt) REVERT: G 122 ILE cc_start: 0.7470 (mm) cc_final: 0.7241 (mm) REVERT: F 10 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7304 (tpt) REVERT: F 58 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6034 (tpp) REVERT: F 69 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6327 (pt) REVERT: F 206 LYS cc_start: 0.6721 (mttt) cc_final: 0.6502 (mttt) REVERT: H 58 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6040 (tpp) REVERT: H 65 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6759 (ptm-80) REVERT: H 206 LYS cc_start: 0.6725 (mttt) cc_final: 0.6511 (mttt) outliers start: 26 outliers final: 7 residues processed: 167 average time/residue: 1.1204 time to fit residues: 202.9895 Evaluate side-chains 159 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.192073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129499 restraints weight = 35117.507| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.75 r_work: 0.2929 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10932 Z= 0.128 Angle : 0.423 7.423 14814 Z= 0.236 Chirality : 0.036 0.130 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.620 27.406 1470 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.31 % Allowed : 17.71 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.23), residues: 1336 helix: 4.13 (0.15), residues: 954 sheet: 0.99 (1.00), residues: 28 loop : -0.23 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS H 205 PHE 0.010 0.001 PHE G 107 TYR 0.011 0.001 TYR G 89 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 864) hydrogen bonds : angle 3.25009 ( 2510) SS BOND : bond 0.00160 ( 8) SS BOND : angle 0.31149 ( 16) covalent geometry : bond 0.00258 (10924) covalent geometry : angle 0.42296 (14798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.216 Fit side-chains REVERT: B 629 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6562 (tpt) REVERT: E 10 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6968 (mmm) REVERT: E 31 ASP cc_start: 0.8273 (m-30) cc_final: 0.7938 (m-30) REVERT: G 74 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6247 (ttpt) REVERT: G 122 ILE cc_start: 0.7480 (mm) cc_final: 0.7255 (mm) REVERT: F 58 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6657 (tpp) REVERT: F 65 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6781 (ptm-80) REVERT: F 69 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6419 (pt) REVERT: F 206 LYS cc_start: 0.6733 (mttt) cc_final: 0.6522 (mttt) REVERT: H 58 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.5984 (tpp) REVERT: H 65 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6750 (ptm-80) REVERT: H 206 LYS cc_start: 0.6738 (mttt) cc_final: 0.6504 (mttt) outliers start: 37 outliers final: 18 residues processed: 164 average time/residue: 1.1114 time to fit residues: 197.7332 Evaluate side-chains 169 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.191930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129765 restraints weight = 30509.315| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.63 r_work: 0.2937 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10932 Z= 0.131 Angle : 0.428 7.783 14814 Z= 0.239 Chirality : 0.036 0.126 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.661 27.926 1470 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.58 % Allowed : 17.35 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.23), residues: 1336 helix: 4.12 (0.15), residues: 954 sheet: 1.15 (1.01), residues: 28 loop : -0.21 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS H 205 PHE 0.010 0.001 PHE G 107 TYR 0.014 0.001 TYR B 523 ARG 0.004 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 864) hydrogen bonds : angle 3.25578 ( 2510) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.31029 ( 16) covalent geometry : bond 0.00267 (10924) covalent geometry : angle 0.42845 (14798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.184 Fit side-chains REVERT: B 629 MET cc_start: 0.6854 (tpp) cc_final: 0.6568 (tpt) REVERT: D 629 MET cc_start: 0.6852 (tpp) cc_final: 0.6583 (tpt) REVERT: E 10 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6939 (mmm) REVERT: E 31 ASP cc_start: 0.8292 (m-30) cc_final: 0.7962 (m-30) REVERT: E 204 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6633 (mtt180) REVERT: G 65 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7461 (ptm160) REVERT: G 74 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6194 (ttpt) REVERT: G 122 ILE cc_start: 0.7548 (mm) cc_final: 0.7314 (mm) REVERT: G 204 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6629 (mtt90) REVERT: F 58 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6027 (tpp) REVERT: F 65 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6782 (ptm-80) REVERT: F 69 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6309 (pt) REVERT: F 206 LYS cc_start: 0.6752 (mttt) cc_final: 0.6547 (mttt) REVERT: H 58 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6114 (tpp) REVERT: H 65 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6782 (ptm-80) REVERT: H 206 LYS cc_start: 0.6771 (mttt) cc_final: 0.6537 (mttt) outliers start: 40 outliers final: 15 residues processed: 167 average time/residue: 1.1757 time to fit residues: 212.3661 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 128 optimal weight: 0.4980 chunk 120 optimal weight: 0.0060 chunk 86 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.193881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131948 restraints weight = 32364.180| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.63 r_work: 0.2973 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10932 Z= 0.105 Angle : 0.395 8.034 14814 Z= 0.219 Chirality : 0.035 0.123 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.465 26.757 1470 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.15 % Allowed : 18.52 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.23), residues: 1336 helix: 4.28 (0.15), residues: 956 sheet: 1.44 (1.07), residues: 28 loop : -0.19 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 PHE 0.008 0.001 PHE C 607 TYR 0.013 0.001 TYR D 523 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 864) hydrogen bonds : angle 3.11533 ( 2510) SS BOND : bond 0.00135 ( 8) SS BOND : angle 0.27777 ( 16) covalent geometry : bond 0.00199 (10924) covalent geometry : angle 0.39507 (14798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.117 Fit side-chains REVERT: B 629 MET cc_start: 0.6839 (tpp) cc_final: 0.6540 (tpt) REVERT: D 629 MET cc_start: 0.6823 (tpp) cc_final: 0.6542 (tpt) REVERT: E 10 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6884 (mmm) REVERT: G 65 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7035 (ptt-90) REVERT: G 74 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6179 (ttpt) REVERT: G 122 ILE cc_start: 0.7428 (mm) cc_final: 0.7194 (mm) REVERT: F 10 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7312 (tpt) REVERT: F 58 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6081 (tpp) REVERT: F 69 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6314 (pt) REVERT: F 206 LYS cc_start: 0.6742 (mttt) cc_final: 0.6529 (mttt) REVERT: H 58 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6232 (tpp) REVERT: H 206 LYS cc_start: 0.6744 (mttt) cc_final: 0.6528 (mttt) outliers start: 24 outliers final: 10 residues processed: 159 average time/residue: 1.1778 time to fit residues: 203.4211 Evaluate side-chains 155 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.192646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130273 restraints weight = 32198.326| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.62 r_work: 0.2949 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10932 Z= 0.120 Angle : 0.417 8.148 14814 Z= 0.231 Chirality : 0.036 0.138 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.548 27.022 1470 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.59 % Allowed : 18.34 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.23), residues: 1336 helix: 4.20 (0.15), residues: 956 sheet: 1.50 (1.05), residues: 28 loop : -0.20 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 33 HIS 0.003 0.000 HIS H 205 PHE 0.010 0.001 PHE G 107 TYR 0.015 0.001 TYR B 523 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 864) hydrogen bonds : angle 3.17058 ( 2510) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.26497 ( 16) covalent geometry : bond 0.00239 (10924) covalent geometry : angle 0.41701 (14798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.167 Fit side-chains REVERT: E 31 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: G 65 ARG cc_start: 0.7853 (ptm-80) cc_final: 0.7352 (ptm-80) REVERT: G 74 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6168 (ttpt) REVERT: G 122 ILE cc_start: 0.7473 (mm) cc_final: 0.7234 (mm) REVERT: F 58 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6640 (tpp) REVERT: F 69 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6411 (pt) REVERT: F 206 LYS cc_start: 0.6737 (mttt) cc_final: 0.6512 (mttt) REVERT: H 58 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6187 (tpp) REVERT: H 65 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6734 (ptm-80) REVERT: H 206 LYS cc_start: 0.6750 (mttt) cc_final: 0.6519 (mttt) outliers start: 29 outliers final: 13 residues processed: 160 average time/residue: 1.1079 time to fit residues: 192.3799 Evaluate side-chains 158 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.194855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132893 restraints weight = 35924.239| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.72 r_work: 0.2986 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10932 Z= 0.099 Angle : 0.388 8.189 14814 Z= 0.214 Chirality : 0.035 0.135 1674 Planarity : 0.003 0.030 1808 Dihedral : 3.364 25.418 1470 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.23), residues: 1336 helix: 4.35 (0.15), residues: 956 sheet: 1.56 (1.08), residues: 28 loop : -0.17 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.003 0.000 HIS H 205 PHE 0.008 0.001 PHE C 607 TYR 0.013 0.001 TYR D 523 ARG 0.003 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 864) hydrogen bonds : angle 3.05229 ( 2510) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.23154 ( 16) covalent geometry : bond 0.00182 (10924) covalent geometry : angle 0.38837 (14798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.036 Fit side-chains REVERT: E 31 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: G 65 ARG cc_start: 0.7856 (ptm-80) cc_final: 0.7344 (ptm-80) REVERT: G 74 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6173 (ttpt) REVERT: G 122 ILE cc_start: 0.7387 (mm) cc_final: 0.7149 (mm) REVERT: F 10 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7318 (tpt) REVERT: F 58 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6091 (tpp) REVERT: F 206 LYS cc_start: 0.6693 (mttt) cc_final: 0.6468 (mttt) REVERT: H 58 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6172 (tpp) REVERT: H 206 LYS cc_start: 0.6702 (mttt) cc_final: 0.6479 (mttt) outliers start: 22 outliers final: 10 residues processed: 158 average time/residue: 1.1089 time to fit residues: 190.1302 Evaluate side-chains 158 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 0.0970 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.191598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129893 restraints weight = 27336.683| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.54 r_work: 0.2928 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10932 Z= 0.144 Angle : 0.448 8.413 14814 Z= 0.249 Chirality : 0.037 0.135 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.517 17.261 1468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.23), residues: 1336 helix: 4.13 (0.15), residues: 954 sheet: 1.35 (0.83), residues: 38 loop : -0.34 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 33 HIS 0.003 0.001 HIS F 205 PHE 0.012 0.001 PHE G 107 TYR 0.014 0.001 TYR D 523 ARG 0.002 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 864) hydrogen bonds : angle 3.24589 ( 2510) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.30850 ( 16) covalent geometry : bond 0.00299 (10924) covalent geometry : angle 0.44782 (14798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.113 Fit side-chains REVERT: E 10 MET cc_start: 0.7311 (tpt) cc_final: 0.6704 (mmm) REVERT: E 31 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: E 204 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6696 (mtt180) REVERT: G 65 ARG cc_start: 0.7859 (ptm-80) cc_final: 0.7601 (ptm-80) REVERT: G 74 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6180 (ttpt) REVERT: G 122 ILE cc_start: 0.7673 (mm) cc_final: 0.7432 (mm) REVERT: G 204 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6663 (mtt180) REVERT: F 58 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6657 (tpp) REVERT: F 206 LYS cc_start: 0.6779 (mttt) cc_final: 0.6549 (mttt) REVERT: H 58 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6670 (tpp) REVERT: H 65 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6842 (ptm-80) REVERT: H 206 LYS cc_start: 0.6806 (mttt) cc_final: 0.6561 (mttt) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 1.2178 time to fit residues: 208.7516 Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129959 restraints weight = 32381.383| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.65 r_work: 0.2939 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10932 Z= 0.127 Angle : 0.429 8.284 14814 Z= 0.238 Chirality : 0.036 0.133 1674 Planarity : 0.003 0.031 1808 Dihedral : 3.467 16.912 1468 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.70 % Allowed : 19.23 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.57 (0.23), residues: 1336 helix: 4.14 (0.15), residues: 956 sheet: 1.35 (0.85), residues: 38 loop : -0.35 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 33 HIS 0.003 0.001 HIS F 205 PHE 0.010 0.001 PHE G 107 TYR 0.015 0.001 TYR D 523 ARG 0.005 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 864) hydrogen bonds : angle 3.19888 ( 2510) SS BOND : bond 0.00162 ( 8) SS BOND : angle 0.28856 ( 16) covalent geometry : bond 0.00255 (10924) covalent geometry : angle 0.42878 (14798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.626 Fit side-chains REVERT: E 10 MET cc_start: 0.7293 (tpt) cc_final: 0.6682 (mmm) REVERT: E 31 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: G 65 ARG cc_start: 0.7805 (ptm-80) cc_final: 0.7547 (ptm-80) REVERT: G 74 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6176 (ttpt) REVERT: G 122 ILE cc_start: 0.7580 (mm) cc_final: 0.7333 (mm) REVERT: G 204 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6573 (mtt180) REVERT: F 58 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6615 (tpp) REVERT: F 206 LYS cc_start: 0.6692 (mttt) cc_final: 0.6479 (mttt) REVERT: H 58 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6657 (tpp) REVERT: H 206 LYS cc_start: 0.6699 (mttt) cc_final: 0.6474 (mttt) outliers start: 19 outliers final: 13 residues processed: 155 average time/residue: 1.2702 time to fit residues: 212.6332 Evaluate side-chains 160 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 821 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.193097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131504 restraints weight = 28653.841| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.54 r_work: 0.2955 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10932 Z= 0.115 Angle : 0.413 8.352 14814 Z= 0.229 Chirality : 0.036 0.132 1674 Planarity : 0.003 0.030 1808 Dihedral : 3.388 16.525 1468 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.79 % Allowed : 19.23 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.23), residues: 1336 helix: 4.22 (0.15), residues: 956 sheet: 0.98 (1.08), residues: 30 loop : -0.17 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.003 0.000 HIS H 205 PHE 0.009 0.001 PHE G 107 TYR 0.014 0.001 TYR D 523 ARG 0.005 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 864) hydrogen bonds : angle 3.14232 ( 2510) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.28315 ( 16) covalent geometry : bond 0.00223 (10924) covalent geometry : angle 0.41309 (14798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8964.70 seconds wall clock time: 154 minutes 32.28 seconds (9272.28 seconds total)