Starting phenix.real_space_refine on Mon Jul 28 21:57:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqb_29382/07_2025/8fqb_29382.cif" } resolution = 2.36 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 74 5.16 5 Cl 2 4.86 5 C 6996 2.51 5 N 1706 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10823 Number of models: 1 Model: "" Number of chains: 19 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: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 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: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 4 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 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 Time building chain proxies: 8.89, per 1000 atoms: 0.82 Number of scatterers: 10823 At special positions: 0 Unit cell: (112.203, 112.203, 90.909, 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 2 17.00 S 74 16.00 O 2044 8.00 N 1706 7.00 C 6996 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: 2.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 73.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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 625 removed outlier: 3.504A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) 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 625 removed outlier: 3.509A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) 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 removed outlier: 3.566A pdb=" N TYR E 96 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.808A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.605A 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: 3.675A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.573A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.822A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.557A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.876A 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: 3.728A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.661A 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: 3.758A 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: 3.753A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.660A 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 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.559A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.557A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2474 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: 3.20 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3226 1.34 - 1.46: 3023 1.46 - 1.58: 4547 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 10910 Sorted by residual: bond pdb=" CB LYS D 826 " pdb=" CG LYS D 826 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB LYS B 826 " pdb=" CG LYS B 826 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CB MET D 825 " pdb=" CG MET D 825 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.87e-01 bond pdb=" CA LYS B 826 " pdb=" CB LYS B 826 " ideal model delta sigma weight residual 1.530 1.547 -0.017 2.00e-02 2.50e+03 7.51e-01 bond pdb=" CA THR H 130 " pdb=" CB THR H 130 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.69e-02 3.50e+03 7.34e-01 ... (remaining 10905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 14600 1.53 - 3.06: 133 3.06 - 4.60: 25 4.60 - 6.13: 10 6.13 - 7.66: 8 Bond angle restraints: 14776 Sorted by residual: angle pdb=" CA LYS B 826 " pdb=" CB LYS B 826 " pdb=" CG LYS B 826 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.48e+00 angle pdb=" CA LYS D 826 " pdb=" CB LYS D 826 " pdb=" CG LYS D 826 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.48e+00 angle pdb=" CB MET B 825 " pdb=" CG MET B 825 " pdb=" SD MET B 825 " ideal model delta sigma weight residual 112.70 120.36 -7.66 3.00e+00 1.11e-01 6.52e+00 angle pdb=" CB MET D 825 " pdb=" CG MET D 825 " pdb=" SD MET D 825 " ideal model delta sigma weight residual 112.70 120.33 -7.63 3.00e+00 1.11e-01 6.47e+00 angle pdb=" CB MET C 585 " pdb=" CG MET C 585 " pdb=" SD MET C 585 " ideal model delta sigma weight residual 112.70 120.12 -7.42 3.00e+00 1.11e-01 6.11e+00 ... (remaining 14771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5363 17.94 - 35.88: 618 35.88 - 53.82: 186 53.82 - 71.75: 42 71.75 - 89.69: 13 Dihedral angle restraints: 6222 sinusoidal: 2296 harmonic: 3926 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 -121.91 35.91 1 1.00e+01 1.00e-02 1.82e+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 -120.89 34.89 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA ASN E 149 " pdb=" CB ASN E 149 " pdb=" CG ASN E 149 " pdb=" OD1 ASN E 149 " ideal model delta sinusoidal sigma weight residual -90.00 -163.48 73.48 2 2.00e+01 2.50e-03 1.10e+01 ... (remaining 6219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1108 0.027 - 0.055: 356 0.055 - 0.082: 164 0.082 - 0.110: 43 0.110 - 0.137: 1 Chirality restraints: 1672 Sorted by residual: chirality pdb=" CB ILE E 153 " pdb=" CA ILE E 153 " pdb=" CG1 ILE E 153 " pdb=" CG2 ILE E 153 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ASP G 88 " pdb=" N ASP G 88 " pdb=" C ASP G 88 " pdb=" CB ASP G 88 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.97e-01 ... (remaining 1669 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO G 108 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO E 108 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 546 " 0.006 2.00e-02 2.50e+03 8.28e-03 1.20e+00 pdb=" CG PHE D 546 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 546 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 546 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 546 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 546 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 546 " 0.001 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 285 2.70 - 3.25: 10586 3.25 - 3.80: 19096 3.80 - 4.35: 22438 4.35 - 4.90: 38137 Nonbonded interactions: 90542 Sorted by model distance: nonbonded pdb=" OE2 GLU A 524 " pdb=" OH TYR E 176 " model vdw 2.144 3.040 nonbonded pdb=" OE2 GLU C 524 " pdb=" OH TYR G 176 " model vdw 2.198 3.040 nonbonded pdb=" NH2 ARG E 102 " pdb=" O HOH E 401 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASN G 149 " pdb=" O HOH G 401 " model vdw 2.240 3.040 nonbonded pdb=" O HOH A 921 " pdb=" O HOH A 927 " model vdw 2.261 3.040 ... (remaining 90537 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)) 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)) 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)) 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)) } 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.460 Find NCS groups from input model: 0.520 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10918 Z= 0.112 Angle : 0.451 7.659 14792 Z= 0.243 Chirality : 0.034 0.137 1672 Planarity : 0.003 0.032 1804 Dihedral : 17.429 89.693 3682 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 24.73 % Favored : 73.48 % 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: 4.04 (0.23), residues: 1330 helix: 3.74 (0.16), residues: 950 sheet: 3.00 (1.53), residues: 10 loop : -0.41 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.002 0.001 HIS G 60 PHE 0.019 0.001 PHE D 546 TYR 0.010 0.001 TYR D 523 ARG 0.004 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.09465 ( 850) hydrogen bonds : angle 4.03085 ( 2474) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.31943 ( 16) covalent geometry : bond 0.00218 (10910) covalent geometry : angle 0.45134 (14776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.218 Fit side-chains REVERT: G 24 MET cc_start: 0.4038 (tpt) cc_final: 0.3095 (tpt) REVERT: G 113 ILE cc_start: 0.7139 (mt) cc_final: 0.6841 (mp) outliers start: 20 outliers final: 18 residues processed: 178 average time/residue: 1.1245 time to fit residues: 219.8746 Evaluate side-chains 178 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.0050 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 0.0670 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 791 ASN E 149 ASN G 149 ASN F 160 ASN H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.248086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.198168 restraints weight = 27364.917| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.65 r_work: 0.3805 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10918 Z= 0.112 Angle : 0.419 5.875 14792 Z= 0.232 Chirality : 0.034 0.113 1672 Planarity : 0.003 0.035 1804 Dihedral : 5.271 57.023 1497 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.05 % Allowed : 22.31 % Favored : 74.64 % 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: 4.16 (0.23), residues: 1330 helix: 3.84 (0.16), residues: 954 sheet: 0.55 (1.16), residues: 20 loop : -0.39 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 178 HIS 0.002 0.001 HIS C 552 PHE 0.013 0.001 PHE E 180 TYR 0.012 0.001 TYR G 181 ARG 0.005 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 850) hydrogen bonds : angle 3.32324 ( 2474) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.38525 ( 16) covalent geometry : bond 0.00214 (10910) covalent geometry : angle 0.41936 (14776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.058 Fit side-chains REVERT: C 811 LEU cc_start: 0.7650 (mm) cc_final: 0.7418 (mt) REVERT: E 12 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5778 (tt) REVERT: G 24 MET cc_start: 0.3704 (tpt) cc_final: 0.2555 (tpt) REVERT: G 113 ILE cc_start: 0.6513 (mt) cc_final: 0.6224 (mp) REVERT: F 149 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7101 (t0) REVERT: F 156 TYR cc_start: 0.8496 (t80) cc_final: 0.8284 (t80) outliers start: 34 outliers final: 21 residues processed: 189 average time/residue: 0.9525 time to fit residues: 197.6567 Evaluate side-chains 185 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 F 160 ASN H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.248650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.199788 restraints weight = 33354.787| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.77 r_work: 0.3800 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10918 Z= 0.105 Angle : 0.403 6.030 14792 Z= 0.222 Chirality : 0.034 0.110 1672 Planarity : 0.003 0.035 1804 Dihedral : 4.126 57.659 1474 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.78 % Allowed : 23.12 % Favored : 74.10 % 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: 4.20 (0.23), residues: 1330 helix: 3.88 (0.16), residues: 954 sheet: 0.79 (1.12), residues: 20 loop : -0.42 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.001 HIS E 205 PHE 0.013 0.001 PHE B 546 TYR 0.011 0.001 TYR G 176 ARG 0.005 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 850) hydrogen bonds : angle 3.21600 ( 2474) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.28445 ( 16) covalent geometry : bond 0.00200 (10910) covalent geometry : angle 0.40348 (14776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 12 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5830 (tt) REVERT: E 76 LEU cc_start: 0.5418 (tp) cc_final: 0.5120 (mt) REVERT: E 120 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4923 (mt) REVERT: E 206 LYS cc_start: 0.6653 (ttmm) cc_final: 0.5924 (tttm) REVERT: G 113 ILE cc_start: 0.6539 (mt) cc_final: 0.6232 (mp) REVERT: F 156 TYR cc_start: 0.8545 (t80) cc_final: 0.8336 (t80) REVERT: H 117 MET cc_start: 0.7126 (mtp) cc_final: 0.6793 (mtp) outliers start: 31 outliers final: 23 residues processed: 191 average time/residue: 1.0640 time to fit residues: 222.0708 Evaluate side-chains 191 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 124 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.247943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198887 restraints weight = 26808.437| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.56 r_work: 0.3798 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10918 Z= 0.111 Angle : 0.416 6.340 14792 Z= 0.228 Chirality : 0.034 0.112 1672 Planarity : 0.003 0.036 1804 Dihedral : 3.932 59.451 1474 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.14 % Allowed : 22.31 % Favored : 74.55 % 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: 4.11 (0.23), residues: 1330 helix: 3.83 (0.16), residues: 954 sheet: -0.21 (1.89), residues: 10 loop : -0.45 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.001 HIS E 205 PHE 0.012 0.001 PHE D 546 TYR 0.009 0.001 TYR G 181 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 850) hydrogen bonds : angle 3.22347 ( 2474) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.25718 ( 16) covalent geometry : bond 0.00216 (10910) covalent geometry : angle 0.41587 (14776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.4960 (pm20) REVERT: D 566 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.4958 (pm20) REVERT: E 12 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5748 (tt) REVERT: E 24 MET cc_start: 0.3428 (tpt) cc_final: 0.2607 (tpt) REVERT: E 120 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4857 (mt) REVERT: E 206 LYS cc_start: 0.6580 (ttmm) cc_final: 0.5839 (tttm) REVERT: G 24 MET cc_start: 0.3660 (tpt) cc_final: 0.2571 (tpt) REVERT: G 113 ILE cc_start: 0.6411 (mt) cc_final: 0.6156 (mp) REVERT: F 117 MET cc_start: 0.7177 (mtp) cc_final: 0.6832 (mtp) REVERT: H 117 MET cc_start: 0.7115 (mtp) cc_final: 0.6747 (mtp) REVERT: H 142 PHE cc_start: 0.8232 (m-80) cc_final: 0.8030 (m-80) outliers start: 35 outliers final: 23 residues processed: 192 average time/residue: 1.1102 time to fit residues: 233.5216 Evaluate side-chains 197 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.246977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.196488 restraints weight = 31779.599| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.90 r_work: 0.3771 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10918 Z= 0.121 Angle : 0.439 8.357 14792 Z= 0.238 Chirality : 0.035 0.115 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.921 59.066 1472 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.87 % Allowed : 22.85 % Favored : 74.28 % 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: 4.05 (0.22), residues: 1330 helix: 3.78 (0.16), residues: 954 sheet: 0.24 (1.98), residues: 10 loop : -0.48 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 578 HIS 0.002 0.001 HIS H 205 PHE 0.015 0.001 PHE D 546 TYR 0.010 0.001 TYR G 181 ARG 0.006 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 850) hydrogen bonds : angle 3.27807 ( 2474) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.95852 ( 16) covalent geometry : bond 0.00241 (10910) covalent geometry : angle 0.43772 (14776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.4960 (pm20) REVERT: C 816 TYR cc_start: 0.6788 (t80) cc_final: 0.6298 (t80) REVERT: D 566 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.4954 (pm20) REVERT: E 12 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5768 (tt) REVERT: E 120 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.4863 (mt) REVERT: E 206 LYS cc_start: 0.6625 (ttmm) cc_final: 0.5867 (tttm) REVERT: G 61 SER cc_start: 0.6229 (OUTLIER) cc_final: 0.5865 (p) REVERT: G 113 ILE cc_start: 0.6422 (mt) cc_final: 0.6186 (mp) REVERT: G 206 LYS cc_start: 0.6682 (ttmm) cc_final: 0.5901 (tttm) REVERT: F 117 MET cc_start: 0.7178 (mtp) cc_final: 0.6791 (mtp) REVERT: F 156 TYR cc_start: 0.8543 (t80) cc_final: 0.8335 (t80) REVERT: H 117 MET cc_start: 0.7122 (mtp) cc_final: 0.6755 (mtp) outliers start: 32 outliers final: 24 residues processed: 193 average time/residue: 1.0279 time to fit residues: 216.8398 Evaluate side-chains 198 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.0770 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.244852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.193075 restraints weight = 26334.288| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.51 r_work: 0.3767 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10918 Z= 0.152 Angle : 0.486 8.099 14792 Z= 0.265 Chirality : 0.037 0.120 1672 Planarity : 0.003 0.038 1804 Dihedral : 4.130 57.226 1472 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.41 % Allowed : 22.13 % Favored : 74.46 % 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: 3.75 (0.22), residues: 1330 helix: 3.54 (0.16), residues: 954 sheet: 0.99 (1.28), residues: 20 loop : -0.62 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 578 HIS 0.003 0.001 HIS H 205 PHE 0.017 0.002 PHE D 546 TYR 0.013 0.001 TYR A 616 ARG 0.006 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.05335 ( 850) hydrogen bonds : angle 3.45898 ( 2474) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.78804 ( 16) covalent geometry : bond 0.00318 (10910) covalent geometry : angle 0.48521 (14776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.4985 (pm20) REVERT: C 816 TYR cc_start: 0.6794 (t80) cc_final: 0.6320 (t80) REVERT: D 566 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.4996 (pm20) REVERT: E 206 LYS cc_start: 0.6571 (ttmm) cc_final: 0.5800 (tttm) REVERT: G 206 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5857 (tttm) REVERT: F 117 MET cc_start: 0.7199 (mtp) cc_final: 0.6849 (mtp) REVERT: H 78 LYS cc_start: 0.6788 (pttp) cc_final: 0.6383 (pttm) REVERT: H 117 MET cc_start: 0.7184 (mtp) cc_final: 0.6879 (mtp) outliers start: 38 outliers final: 30 residues processed: 197 average time/residue: 1.2960 time to fit residues: 279.3814 Evaluate side-chains 197 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 204 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 82 optimal weight: 0.0070 chunk 85 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.249786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.201034 restraints weight = 31173.362| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.77 r_work: 0.3826 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10918 Z= 0.098 Angle : 0.411 6.941 14792 Z= 0.221 Chirality : 0.034 0.112 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.674 59.662 1472 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.88 % Allowed : 23.21 % Favored : 74.91 % 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: 4.20 (0.23), residues: 1330 helix: 3.94 (0.16), residues: 954 sheet: 0.21 (2.09), residues: 10 loop : -0.54 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.002 0.000 HIS E 205 PHE 0.018 0.001 PHE B 546 TYR 0.012 0.001 TYR G 176 ARG 0.006 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 850) hydrogen bonds : angle 3.12853 ( 2474) SS BOND : bond 0.00200 ( 8) SS BOND : angle 0.61918 ( 16) covalent geometry : bond 0.00184 (10910) covalent geometry : angle 0.41035 (14776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 816 TYR cc_start: 0.6739 (t80) cc_final: 0.6265 (t80) REVERT: E 24 MET cc_start: 0.3523 (tpt) cc_final: 0.3186 (tpt) REVERT: E 206 LYS cc_start: 0.6571 (ttmm) cc_final: 0.5830 (tttm) REVERT: G 24 MET cc_start: 0.3716 (tpt) cc_final: 0.2692 (tpt) REVERT: G 113 ILE cc_start: 0.6415 (mt) cc_final: 0.6153 (mp) REVERT: G 131 ARG cc_start: 0.5544 (mmp-170) cc_final: 0.5309 (mmm160) REVERT: G 206 LYS cc_start: 0.6650 (ttmm) cc_final: 0.5878 (tttm) REVERT: F 117 MET cc_start: 0.7093 (mtp) cc_final: 0.6709 (mtp) REVERT: F 156 TYR cc_start: 0.8512 (t80) cc_final: 0.8298 (t80) REVERT: H 117 MET cc_start: 0.6987 (mtp) cc_final: 0.6614 (mtp) outliers start: 21 outliers final: 15 residues processed: 184 average time/residue: 1.0286 time to fit residues: 207.0122 Evaluate side-chains 183 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.245361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194452 restraints weight = 30515.907| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.66 r_work: 0.3759 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10918 Z= 0.140 Angle : 0.474 7.963 14792 Z= 0.256 Chirality : 0.036 0.115 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.896 57.898 1471 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.69 % Allowed : 22.94 % Favored : 74.37 % 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: 3.90 (0.23), residues: 1330 helix: 3.67 (0.16), residues: 956 sheet: 0.94 (1.29), residues: 20 loop : -0.65 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS F 205 PHE 0.012 0.002 PHE E 180 TYR 0.011 0.001 TYR A 616 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 850) hydrogen bonds : angle 3.36109 ( 2474) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.67054 ( 16) covalent geometry : bond 0.00289 (10910) covalent geometry : angle 0.47346 (14776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.4958 (pm20) REVERT: B 629 MET cc_start: 0.5932 (tpp) cc_final: 0.5331 (tpt) REVERT: C 816 TYR cc_start: 0.6825 (t80) cc_final: 0.6368 (t80) REVERT: D 566 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.4956 (pm20) REVERT: E 24 MET cc_start: 0.3531 (tpt) cc_final: 0.2853 (tpt) REVERT: E 206 LYS cc_start: 0.6615 (ttmm) cc_final: 0.5842 (tttm) REVERT: G 113 ILE cc_start: 0.6572 (mt) cc_final: 0.6291 (mp) REVERT: G 206 LYS cc_start: 0.6659 (ttmm) cc_final: 0.5899 (tttm) REVERT: F 117 MET cc_start: 0.7209 (mtp) cc_final: 0.6892 (mtp) REVERT: H 78 LYS cc_start: 0.6768 (pttp) cc_final: 0.6380 (pttm) REVERT: H 117 MET cc_start: 0.7123 (mtp) cc_final: 0.6811 (mtp) outliers start: 30 outliers final: 21 residues processed: 188 average time/residue: 1.0357 time to fit residues: 212.8105 Evaluate side-chains 189 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 ASN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.245307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.193532 restraints weight = 24119.656| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.28 r_work: 0.3804 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10918 Z= 0.137 Angle : 0.475 7.790 14792 Z= 0.257 Chirality : 0.036 0.115 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.884 57.224 1471 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.78 % Allowed : 22.76 % Favored : 74.46 % 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: 3.80 (0.22), residues: 1330 helix: 3.60 (0.16), residues: 954 sheet: 1.02 (1.31), residues: 20 loop : -0.67 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.002 0.001 HIS H 82 PHE 0.016 0.002 PHE B 546 TYR 0.011 0.001 TYR A 616 ARG 0.007 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 850) hydrogen bonds : angle 3.36499 ( 2474) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.62194 ( 16) covalent geometry : bond 0.00281 (10910) covalent geometry : angle 0.47520 (14776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5009 (pm20) REVERT: B 629 MET cc_start: 0.5974 (tpp) cc_final: 0.5386 (tpt) REVERT: C 816 TYR cc_start: 0.6791 (t80) cc_final: 0.6347 (t80) REVERT: D 566 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5034 (pm20) REVERT: E 206 LYS cc_start: 0.6582 (ttmm) cc_final: 0.5805 (tttm) REVERT: G 206 LYS cc_start: 0.6634 (ttmm) cc_final: 0.5864 (tttm) REVERT: F 117 MET cc_start: 0.7218 (mtp) cc_final: 0.6909 (mtp) REVERT: H 78 LYS cc_start: 0.6816 (pttp) cc_final: 0.6407 (pttm) REVERT: H 117 MET cc_start: 0.7130 (mtp) cc_final: 0.6829 (mtp) outliers start: 31 outliers final: 23 residues processed: 182 average time/residue: 1.0504 time to fit residues: 208.5515 Evaluate side-chains 186 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.0010 chunk 86 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.248091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194079 restraints weight = 20720.843| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.83 r_work: 0.3883 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10918 Z= 0.105 Angle : 0.442 9.395 14792 Z= 0.233 Chirality : 0.034 0.122 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.669 58.644 1471 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.79 % Allowed : 23.84 % Favored : 74.37 % 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: 4.11 (0.23), residues: 1330 helix: 3.87 (0.16), residues: 954 sheet: 0.92 (1.28), residues: 20 loop : -0.64 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS E 205 PHE 0.016 0.001 PHE B 546 TYR 0.009 0.001 TYR G 181 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 850) hydrogen bonds : angle 3.16588 ( 2474) SS BOND : bond 0.00132 ( 8) SS BOND : angle 0.57539 ( 16) covalent geometry : bond 0.00203 (10910) covalent geometry : angle 0.44183 (14776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5070 (pm20) REVERT: B 629 MET cc_start: 0.5899 (tpp) cc_final: 0.5342 (tpt) REVERT: C 816 TYR cc_start: 0.6709 (t80) cc_final: 0.6275 (t80) REVERT: D 566 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5092 (pm20) REVERT: E 24 MET cc_start: 0.3677 (tpt) cc_final: 0.3000 (tpt) REVERT: E 76 LEU cc_start: 0.5583 (tp) cc_final: 0.5208 (mt) REVERT: E 206 LYS cc_start: 0.6615 (ttmm) cc_final: 0.5859 (tttm) REVERT: G 24 MET cc_start: 0.3803 (tpt) cc_final: 0.3459 (tpt) REVERT: G 113 ILE cc_start: 0.6559 (mt) cc_final: 0.6296 (mp) REVERT: G 206 LYS cc_start: 0.6667 (ttmm) cc_final: 0.5927 (tttm) REVERT: F 117 MET cc_start: 0.7041 (mtp) cc_final: 0.6721 (mtp) REVERT: H 117 MET cc_start: 0.6954 (mtp) cc_final: 0.6649 (mtp) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 1.4284 time to fit residues: 275.9516 Evaluate side-chains 178 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.246613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196198 restraints weight = 30004.923| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.47 r_work: 0.3800 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10918 Z= 0.124 Angle : 0.459 7.971 14792 Z= 0.246 Chirality : 0.035 0.125 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.701 58.137 1467 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.06 % Allowed : 23.92 % Favored : 74.01 % 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: 3.97 (0.23), residues: 1330 helix: 3.76 (0.16), residues: 954 sheet: 0.96 (1.27), residues: 20 loop : -0.68 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.001 HIS H 205 PHE 0.012 0.001 PHE E 180 TYR 0.010 0.001 TYR A 616 ARG 0.007 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 850) hydrogen bonds : angle 3.26676 ( 2474) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.56782 ( 16) covalent geometry : bond 0.00251 (10910) covalent geometry : angle 0.45895 (14776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11552.41 seconds wall clock time: 207 minutes 55.66 seconds (12475.66 seconds total)