Starting phenix.real_space_refine on Tue May 13 16:27:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqb_29382/05_2025/8fqb_29382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqb_29382/05_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_29382/05_2025/8fqb_29382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqb_29382/05_2025/8fqb_29382.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqb_29382/05_2025/8fqb_29382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqb_29382/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.30, per 1000 atoms: 0.77 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: 2.33 Conformation dependent library (CDL) restraints added in 1.7 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: 0.91 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: 3.26 Time building geometry restraints manager: 2.73 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.870 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- 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 : 1.091 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: 1.0082 time to fit residues: 196.4155 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 : 1.075 ------------------------------------------------------------------------------- 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 = 27364.921| |-----------------------------------------------------------------------------| 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 1.095 Fit side-chains REVERT: C 811 LEU cc_start: 0.7648 (mm) cc_final: 0.7417 (mt) REVERT: E 12 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5780 (tt) REVERT: G 24 MET cc_start: 0.3699 (tpt) cc_final: 0.2552 (tpt) REVERT: G 113 ILE cc_start: 0.6509 (mt) cc_final: 0.6220 (mp) REVERT: F 149 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7105 (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: 0.9979 time to fit residues: 206.6901 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 : 1.086 ------------------------------------------------------------------------------- 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: 0.6980 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.248378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.198717 restraints weight = 33341.090| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.86 r_work: 0.3794 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0867 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= 0.107 Angle : 0.407 6.085 14792 Z= 0.224 Chirality : 0.034 0.111 1672 Planarity : 0.003 0.036 1804 Dihedral : 4.140 58.088 1474 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.87 % Allowed : 22.94 % Favored : 74.19 % 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: 4.18 (0.23), residues: 1330 helix: 3.86 (0.16), residues: 954 sheet: 0.80 (1.12), residues: 20 loop : -0.43 (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 0.006 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 850) hydrogen bonds : angle 3.23154 ( 2474) SS BOND : bond 0.00261 ( 8) SS BOND : angle 0.27830 ( 16) covalent geometry : bond 0.00205 (10910) covalent geometry : angle 0.40683 (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: 32 poor density : 170 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 12 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5819 (tt) REVERT: E 120 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4920 (mt) REVERT: E 206 LYS cc_start: 0.6653 (ttmm) cc_final: 0.5924 (tttm) REVERT: G 113 ILE cc_start: 0.6565 (mt) cc_final: 0.6278 (mp) REVERT: F 156 TYR cc_start: 0.8549 (t80) cc_final: 0.8334 (t80) REVERT: H 117 MET cc_start: 0.7114 (mtp) cc_final: 0.6779 (mtp) outliers start: 32 outliers final: 24 residues processed: 190 average time/residue: 0.9516 time to fit residues: 198.2927 Evaluate side-chains 193 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 527 MET 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: 7.9990 chunk 74 optimal weight: 0.7980 chunk 124 optimal weight: 0.0270 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4713 r_free = 0.4713 target = 0.247799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198761 restraints weight = 26038.481| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.52 r_work: 0.3800 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 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 = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10918 Z= 0.113 Angle : 0.418 6.178 14792 Z= 0.229 Chirality : 0.034 0.112 1672 Planarity : 0.003 0.036 1804 Dihedral : 3.961 59.736 1474 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.05 % Allowed : 22.85 % 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: 4.11 (0.23), residues: 1330 helix: 3.82 (0.16), residues: 954 sheet: 0.96 (1.20), residues: 20 loop : -0.50 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 178 HIS 0.002 0.001 HIS H 205 PHE 0.012 0.001 PHE B 546 TYR 0.009 0.001 TYR G 181 ARG 0.006 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 850) hydrogen bonds : angle 3.23379 ( 2474) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.25409 ( 16) covalent geometry : bond 0.00220 (10910) covalent geometry : angle 0.41800 (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 208 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.4992 (pm20) REVERT: D 566 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.4986 (pm20) REVERT: E 12 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5797 (tt) REVERT: E 24 MET cc_start: 0.3516 (tpt) cc_final: 0.2671 (tpt) REVERT: E 120 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.4954 (mt) REVERT: E 206 LYS cc_start: 0.6620 (ttmm) cc_final: 0.5877 (tttm) REVERT: G 24 MET cc_start: 0.3798 (tpt) cc_final: 0.2751 (tpt) REVERT: G 113 ILE cc_start: 0.6448 (mt) cc_final: 0.6184 (mp) REVERT: F 117 MET cc_start: 0.7187 (mtp) cc_final: 0.6854 (mtp) REVERT: H 117 MET cc_start: 0.7131 (mtp) cc_final: 0.6767 (mtp) REVERT: H 142 PHE cc_start: 0.8237 (m-80) cc_final: 0.8027 (m-80) outliers start: 34 outliers final: 23 residues processed: 193 average time/residue: 0.9755 time to fit residues: 206.3945 Evaluate side-chains 200 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 90 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4709 r_free = 0.4709 target = 0.247353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.197710 restraints weight = 31991.657| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.66 r_work: 0.3788 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1015 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= 0.116 Angle : 0.432 8.180 14792 Z= 0.234 Chirality : 0.035 0.114 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.885 59.193 1472 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.87 % Allowed : 23.21 % Favored : 73.92 % 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: 4.08 (0.23), residues: 1330 helix: 3.81 (0.16), residues: 954 sheet: 0.26 (2.00), residues: 10 loop : -0.49 (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 H 205 PHE 0.015 0.001 PHE D 546 TYR 0.009 0.001 TYR G 181 ARG 0.006 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 850) hydrogen bonds : angle 3.25179 ( 2474) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.93061 ( 16) covalent geometry : bond 0.00229 (10910) covalent geometry : angle 0.43135 (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 201 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.4973 (pm20) REVERT: C 816 TYR cc_start: 0.6777 (t80) cc_final: 0.6288 (t80) REVERT: D 566 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.4968 (pm20) REVERT: E 12 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5790 (tt) REVERT: E 120 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4908 (mt) REVERT: E 206 LYS cc_start: 0.6629 (ttmm) cc_final: 0.5875 (tttm) REVERT: G 61 SER cc_start: 0.6187 (OUTLIER) cc_final: 0.5816 (p) REVERT: G 113 ILE cc_start: 0.6432 (mt) cc_final: 0.6199 (mp) REVERT: G 206 LYS cc_start: 0.6691 (ttmm) cc_final: 0.5913 (tttm) REVERT: F 117 MET cc_start: 0.7181 (mtp) cc_final: 0.6792 (mtp) REVERT: H 117 MET cc_start: 0.7102 (mtp) cc_final: 0.6735 (mtp) outliers start: 32 outliers final: 23 residues processed: 189 average time/residue: 1.0217 time to fit residues: 210.7256 Evaluate side-chains 196 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 126 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4696 r_free = 0.4696 target = 0.245947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194476 restraints weight = 26476.379| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.49 r_work: 0.3785 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1173 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= 0.133 Angle : 0.463 8.211 14792 Z= 0.250 Chirality : 0.036 0.115 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.972 58.029 1472 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.23 % Allowed : 22.40 % 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: 3.91 (0.22), residues: 1330 helix: 3.67 (0.16), residues: 954 sheet: 1.21 (1.29), residues: 20 loop : -0.60 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS H 205 PHE 0.016 0.001 PHE D 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 0.04944 ( 850) hydrogen bonds : angle 3.36027 ( 2474) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.74513 ( 16) covalent geometry : bond 0.00271 (10910) covalent geometry : angle 0.46225 (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 211 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5012 (pm20) REVERT: C 816 TYR cc_start: 0.6809 (t80) cc_final: 0.6347 (t80) REVERT: D 566 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5007 (pm20) REVERT: E 24 MET cc_start: 0.3527 (tpt) cc_final: 0.2859 (tpt) REVERT: E 120 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5004 (mt) REVERT: E 206 LYS cc_start: 0.6644 (ttmm) cc_final: 0.5875 (tttm) REVERT: G 113 ILE cc_start: 0.6537 (mt) cc_final: 0.6283 (mp) REVERT: G 206 LYS cc_start: 0.6675 (ttmm) cc_final: 0.5920 (tttm) REVERT: F 117 MET cc_start: 0.7223 (mtp) cc_final: 0.6841 (mtp) REVERT: F 156 TYR cc_start: 0.8530 (t80) cc_final: 0.8317 (t80) REVERT: H 117 MET cc_start: 0.7141 (mtp) cc_final: 0.6831 (mtp) outliers start: 36 outliers final: 28 residues processed: 197 average time/residue: 1.0292 time to fit residues: 222.1152 Evaluate side-chains 199 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 155 VAL 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: 0.0870 chunk 57 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 chunk 82 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.248588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200201 restraints weight = 31391.630| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.72 r_work: 0.3804 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1180 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= 0.104 Angle : 0.420 6.923 14792 Z= 0.225 Chirality : 0.034 0.124 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.701 59.957 1472 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.69 % Allowed : 23.12 % Favored : 74.19 % 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: 4.14 (0.23), residues: 1330 helix: 3.88 (0.16), residues: 954 sheet: 0.35 (2.05), residues: 10 loop : -0.54 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.003 0.000 HIS E 205 PHE 0.018 0.001 PHE B 546 TYR 0.010 0.001 TYR G 176 ARG 0.007 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 850) hydrogen bonds : angle 3.16026 ( 2474) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.59759 ( 16) covalent geometry : bond 0.00196 (10910) covalent geometry : angle 0.41946 (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 204 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.4906 (pm20) REVERT: C 816 TYR cc_start: 0.6742 (t80) cc_final: 0.6270 (t80) REVERT: D 566 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.4915 (pm20) REVERT: E 206 LYS cc_start: 0.6567 (ttmm) cc_final: 0.5831 (tttm) REVERT: G 113 ILE cc_start: 0.6474 (mt) cc_final: 0.6210 (mp) REVERT: G 131 ARG cc_start: 0.5524 (mmp-170) cc_final: 0.5300 (mmm160) REVERT: G 206 LYS cc_start: 0.6645 (ttmm) cc_final: 0.5877 (tttm) REVERT: F 117 MET cc_start: 0.7111 (mtp) cc_final: 0.6774 (mtp) REVERT: F 156 TYR cc_start: 0.8551 (t80) cc_final: 0.8333 (t80) REVERT: H 117 MET cc_start: 0.7053 (mtp) cc_final: 0.6728 (mtp) outliers start: 30 outliers final: 23 residues processed: 194 average time/residue: 1.0106 time to fit residues: 214.6036 Evaluate side-chains 192 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4703 r_free = 0.4703 target = 0.246664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.196526 restraints weight = 30819.376| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.68 r_work: 0.3778 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 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 = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1229 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= 0.123 Angle : 0.450 7.193 14792 Z= 0.242 Chirality : 0.035 0.122 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.775 59.095 1471 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.87 % Allowed : 23.21 % Favored : 73.92 % 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: 4.02 (0.23), residues: 1330 helix: 3.78 (0.16), residues: 954 sheet: 1.08 (1.29), residues: 20 loop : -0.63 (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 G 60 PHE 0.012 0.001 PHE E 180 TYR 0.009 0.001 TYR G 181 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 850) hydrogen bonds : angle 3.27280 ( 2474) SS BOND : bond 0.00202 ( 8) SS BOND : angle 0.62397 ( 16) covalent geometry : bond 0.00245 (10910) covalent geometry : angle 0.44947 (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: 32 poor density : 167 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.4960 (pm20) REVERT: B 629 MET cc_start: 0.5902 (tpp) cc_final: 0.5306 (tpt) REVERT: C 816 TYR cc_start: 0.6797 (t80) cc_final: 0.6348 (t80) REVERT: D 566 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.4943 (pm20) REVERT: E 24 MET cc_start: 0.3672 (tpt) cc_final: 0.3065 (tpt) REVERT: E 206 LYS cc_start: 0.6628 (ttmm) cc_final: 0.5865 (tttm) REVERT: G 113 ILE cc_start: 0.6452 (mt) cc_final: 0.6194 (mp) REVERT: G 206 LYS cc_start: 0.6683 (ttmm) cc_final: 0.5929 (tttm) REVERT: F 117 MET cc_start: 0.7160 (mtp) cc_final: 0.6830 (mtp) REVERT: F 156 TYR cc_start: 0.8554 (t80) cc_final: 0.8350 (t80) REVERT: H 117 MET cc_start: 0.7047 (mtp) cc_final: 0.6733 (mtp) outliers start: 32 outliers final: 26 residues processed: 189 average time/residue: 0.9949 time to fit residues: 206.1632 Evaluate side-chains 194 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 130 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.246609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.196709 restraints weight = 25046.275| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.37 r_work: 0.3807 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 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 = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1262 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= 0.123 Angle : 0.454 7.381 14792 Z= 0.244 Chirality : 0.035 0.119 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.764 58.882 1471 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 3.98 (0.22), residues: 1330 helix: 3.75 (0.16), residues: 954 sheet: 1.06 (1.31), residues: 20 loop : -0.66 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS F 205 PHE 0.012 0.001 PHE E 180 TYR 0.010 0.001 TYR G 181 ARG 0.007 0.000 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 850) hydrogen bonds : angle 3.27758 ( 2474) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.57271 ( 16) covalent geometry : bond 0.00246 (10910) covalent geometry : angle 0.45422 (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 197 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.4970 (pm20) REVERT: B 629 MET cc_start: 0.5938 (tpp) cc_final: 0.5356 (tpt) REVERT: C 816 TYR cc_start: 0.6799 (t80) cc_final: 0.6378 (t80) REVERT: D 566 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.4984 (pm20) REVERT: E 206 LYS cc_start: 0.6613 (ttmm) cc_final: 0.5848 (tttm) REVERT: G 24 MET cc_start: 0.3838 (tpt) cc_final: 0.3409 (tpt) REVERT: G 113 ILE cc_start: 0.6529 (mt) cc_final: 0.6273 (mp) REVERT: G 206 LYS cc_start: 0.6663 (ttmm) cc_final: 0.5912 (tttm) REVERT: F 117 MET cc_start: 0.7179 (mtp) cc_final: 0.6851 (mtp) REVERT: F 156 TYR cc_start: 0.8534 (t80) cc_final: 0.8316 (t80) REVERT: H 117 MET cc_start: 0.7067 (mtp) cc_final: 0.6765 (mtp) outliers start: 31 outliers final: 27 residues processed: 187 average time/residue: 0.9616 time to fit residues: 197.1630 Evaluate side-chains 192 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 175 SER 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 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL 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: 0.0050 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.4711 r_free = 0.4711 target = 0.247741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.194076 restraints weight = 20778.370| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 4.15 r_work: 0.3866 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1279 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= 0.110 Angle : 0.445 8.104 14792 Z= 0.236 Chirality : 0.035 0.122 1672 Planarity : 0.003 0.038 1804 Dihedral : 3.616 59.550 1467 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.60 % Allowed : 23.48 % Favored : 73.92 % 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: 4.09 (0.22), residues: 1330 helix: 3.85 (0.16), residues: 954 sheet: 0.20 (2.09), residues: 10 loop : -0.58 (0.28), residues: 366 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 0.011 0.001 PHE G 180 TYR 0.009 0.001 TYR G 181 ARG 0.007 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 850) hydrogen bonds : angle 3.19797 ( 2474) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.53363 ( 16) covalent geometry : bond 0.00214 (10910) covalent geometry : angle 0.44464 (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 191 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5030 (pm20) REVERT: B 629 MET cc_start: 0.5886 (tpp) cc_final: 0.5339 (tpt) REVERT: C 816 TYR cc_start: 0.6751 (t80) cc_final: 0.6336 (t80) REVERT: D 566 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5042 (pm20) REVERT: E 24 MET cc_start: 0.3676 (tpt) cc_final: 0.3371 (tpt) REVERT: E 206 LYS cc_start: 0.6591 (ttmm) cc_final: 0.5838 (tttm) REVERT: G 24 MET cc_start: 0.3779 (tpt) cc_final: 0.3363 (tpt) REVERT: G 113 ILE cc_start: 0.6459 (mt) cc_final: 0.6198 (mp) REVERT: G 206 LYS cc_start: 0.6632 (ttmm) cc_final: 0.5890 (tttm) REVERT: F 117 MET cc_start: 0.7096 (mtp) cc_final: 0.6764 (mtp) REVERT: H 117 MET cc_start: 0.7017 (mtp) cc_final: 0.6697 (mtp) outliers start: 29 outliers final: 25 residues processed: 182 average time/residue: 1.0326 time to fit residues: 205.1613 Evaluate side-chains 189 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 175 SER 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 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL 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: 0.9990 chunk 111 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.4699 r_free = 0.4699 target = 0.246342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.196129 restraints weight = 30281.870| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.57 r_work: 0.3790 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10918 Z= 0.126 Angle : 0.470 8.364 14792 Z= 0.249 Chirality : 0.035 0.118 1672 Planarity : 0.003 0.037 1804 Dihedral : 3.711 58.859 1467 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.69 % Allowed : 23.21 % 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: 3.96 (0.22), residues: 1330 helix: 3.74 (0.16), residues: 954 sheet: 0.99 (1.28), residues: 20 loop : -0.68 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 178 HIS 0.002 0.001 HIS F 205 PHE 0.016 0.001 PHE B 546 TYR 0.010 0.001 TYR A 616 ARG 0.007 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 850) hydrogen bonds : angle 3.28835 ( 2474) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.57509 ( 16) covalent geometry : bond 0.00256 (10910) covalent geometry : angle 0.46967 (14776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10104.83 seconds wall clock time: 174 minutes 2.94 seconds (10442.94 seconds total)