Starting phenix.real_space_refine on Wed Mar 4 04:08:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqb_29382/03_2026/8fqb_29382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqb_29382/03_2026/8fqb_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_29382/03_2026/8fqb_29382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqb_29382/03_2026/8fqb_29382.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqb_29382/03_2026/8fqb_29382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqb_29382/03_2026/8fqb_29382.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.78, per 1000 atoms: 0.26 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: 0.87 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 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: 0.29 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: 1.74 Time building geometry restraints manager: 1.07 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: 2.900 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.004 0.000 ARG F 65 TYR 0.010 0.001 TYR D 523 PHE 0.019 0.001 PHE D 546 TRP 0.008 0.001 TRP G 178 HIS 0.002 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00218 (10910) covalent geometry : angle 0.45134 (14776) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.31943 ( 16) hydrogen bonds : bond 0.09465 ( 850) hydrogen bonds : angle 4.03085 ( 2474) *********************** 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 : 0.332 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: 0.4589 time to fit residues: 89.1171 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 : 0.328 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.4712 r_free = 0.4712 target = 0.247606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.198089 restraints weight = 31877.055| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 3.76 r_work: 0.3781 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.0658 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= 0.117 Angle : 0.426 5.805 14792 Z= 0.236 Chirality : 0.035 0.113 1672 Planarity : 0.003 0.035 1804 Dihedral : 5.356 57.627 1497 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.05 % Allowed : 22.40 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.23), residues: 1330 helix: 3.79 (0.16), residues: 954 sheet: 0.56 (1.16), residues: 20 loop : -0.41 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 65 TYR 0.012 0.001 TYR G 181 PHE 0.013 0.001 PHE E 180 TRP 0.009 0.001 TRP G 178 HIS 0.002 0.001 HIS C 552 Details of bonding type rmsd covalent geometry : bond 0.00227 (10910) covalent geometry : angle 0.42604 (14776) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.37198 ( 16) hydrogen bonds : bond 0.04535 ( 850) hydrogen bonds : angle 3.36656 ( 2474) *********************** 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 : 0.376 Fit side-chains REVERT: C 811 LEU cc_start: 0.7682 (mm) cc_final: 0.7455 (mt) REVERT: E 12 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5794 (tt) REVERT: G 24 MET cc_start: 0.3745 (tpt) cc_final: 0.2669 (tpt) REVERT: G 113 ILE cc_start: 0.6582 (mt) cc_final: 0.6269 (mp) REVERT: F 156 TYR cc_start: 0.8518 (t80) cc_final: 0.8296 (t80) REVERT: H 156 TYR cc_start: 0.8524 (t80) cc_final: 0.8321 (t80) outliers start: 34 outliers final: 20 residues processed: 189 average time/residue: 0.3996 time to fit residues: 83.2310 Evaluate side-chains 184 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.245526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194585 restraints weight = 27456.266| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.65 r_work: 0.3767 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10918 Z= 0.141 Angle : 0.457 5.372 14792 Z= 0.255 Chirality : 0.036 0.122 1672 Planarity : 0.003 0.039 1804 Dihedral : 4.529 58.075 1474 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.67 % Allowed : 21.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.22), residues: 1330 helix: 3.57 (0.16), residues: 952 sheet: 0.72 (1.11), residues: 20 loop : -0.57 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 65 TYR 0.012 0.001 TYR A 616 PHE 0.014 0.001 PHE E 180 TRP 0.008 0.001 TRP B 578 HIS 0.003 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00289 (10910) covalent geometry : angle 0.45670 (14776) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.35177 ( 16) hydrogen bonds : bond 0.05197 ( 850) hydrogen bonds : angle 3.48333 ( 2474) *********************** 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 213 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5028 (pm20) REVERT: C 811 LEU cc_start: 0.7640 (mm) cc_final: 0.7439 (mt) REVERT: D 566 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5013 (pm20) REVERT: E 120 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5022 (mt) REVERT: E 206 LYS cc_start: 0.6616 (ttmm) cc_final: 0.5842 (tttm) REVERT: G 113 ILE cc_start: 0.6602 (mt) cc_final: 0.6334 (mp) REVERT: H 117 MET cc_start: 0.7191 (mtp) cc_final: 0.6872 (mtp) outliers start: 41 outliers final: 30 residues processed: 198 average time/residue: 0.4812 time to fit residues: 103.6821 Evaluate side-chains 199 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 153 ILE 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 149 ASN 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 42 THR 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 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 103 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.246443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.195975 restraints weight = 27629.688| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.62 r_work: 0.3779 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 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 = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10918 Z= 0.121 Angle : 0.433 5.790 14792 Z= 0.239 Chirality : 0.035 0.116 1672 Planarity : 0.003 0.040 1804 Dihedral : 4.264 58.735 1474 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.78 % Allowed : 22.67 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.22), residues: 1330 helix: 3.67 (0.16), residues: 952 sheet: 0.78 (1.14), residues: 20 loop : -0.62 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 65 TYR 0.010 0.001 TYR G 181 PHE 0.014 0.001 PHE E 180 TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00240 (10910) covalent geometry : angle 0.43353 (14776) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.30307 ( 16) hydrogen bonds : bond 0.04697 ( 850) hydrogen bonds : angle 3.35371 ( 2474) *********************** 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 199 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 811 LEU cc_start: 0.7691 (mm) cc_final: 0.7476 (mt) REVERT: E 12 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5920 (mm) REVERT: E 120 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4909 (mt) REVERT: E 206 LYS cc_start: 0.6619 (ttmm) cc_final: 0.5853 (tttm) REVERT: G 113 ILE cc_start: 0.6609 (mt) cc_final: 0.6323 (mp) REVERT: F 117 MET cc_start: 0.7226 (mtp) cc_final: 0.6943 (mtp) REVERT: H 78 LYS cc_start: 0.6843 (pttp) cc_final: 0.6443 (pttm) REVERT: H 117 MET cc_start: 0.7169 (mtp) cc_final: 0.6786 (mtp) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.4759 time to fit residues: 97.7317 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 120 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4675 r_free = 0.4675 target = 0.243520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.204157 restraints weight = 22288.487| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 4.62 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4316 r_free = 0.4316 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4316 r_free = 0.4316 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10918 Z= 0.182 Angle : 0.514 6.447 14792 Z= 0.285 Chirality : 0.038 0.138 1672 Planarity : 0.004 0.042 1804 Dihedral : 4.578 55.932 1474 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.85 % Allowed : 21.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.22), residues: 1330 helix: 3.26 (0.16), residues: 952 sheet: 0.59 (1.22), residues: 20 loop : -0.68 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 65 TYR 0.015 0.002 TYR E 181 PHE 0.015 0.002 PHE E 180 TRP 0.011 0.002 TRP D 578 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00391 (10910) covalent geometry : angle 0.51433 (14776) SS BOND : bond 0.00284 ( 8) SS BOND : angle 0.41378 ( 16) hydrogen bonds : bond 0.05849 ( 850) hydrogen bonds : angle 3.63458 ( 2474) *********************** 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 206 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5171 (pm20) REVERT: D 566 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5145 (pm20) REVERT: E 206 LYS cc_start: 0.7110 (ttmm) cc_final: 0.6506 (tttm) REVERT: G 206 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6498 (tttm) REVERT: F 117 MET cc_start: 0.6999 (mtp) cc_final: 0.6798 (mtp) REVERT: H 117 MET cc_start: 0.6998 (mtp) cc_final: 0.6786 (mtp) outliers start: 43 outliers final: 35 residues processed: 190 average time/residue: 0.5016 time to fit residues: 103.6266 Evaluate side-chains 194 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 ARG 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 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 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 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 160 ASN 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 23 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.246125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.196253 restraints weight = 32392.006| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.71 r_work: 0.3767 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1234 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 : 0.449 7.105 14792 Z= 0.245 Chirality : 0.035 0.120 1672 Planarity : 0.003 0.041 1804 Dihedral : 4.173 56.870 1474 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.14 % Allowed : 21.68 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.22), residues: 1330 helix: 3.59 (0.16), residues: 954 sheet: 0.63 (1.24), residues: 20 loop : -0.72 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 65 TYR 0.010 0.001 TYR E 181 PHE 0.014 0.001 PHE E 180 TRP 0.009 0.001 TRP E 178 HIS 0.002 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00252 (10910) covalent geometry : angle 0.44898 (14776) SS BOND : bond 0.00205 ( 8) SS BOND : angle 0.29503 ( 16) hydrogen bonds : bond 0.04748 ( 850) hydrogen bonds : angle 3.35936 ( 2474) *********************** 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 199 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.4946 (pm20) REVERT: B 629 MET cc_start: 0.5978 (tpp) cc_final: 0.5598 (tpt) REVERT: D 566 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.4961 (pm20) REVERT: E 206 LYS cc_start: 0.6636 (ttmm) cc_final: 0.5875 (tttm) REVERT: G 206 LYS cc_start: 0.6650 (ttmm) cc_final: 0.5889 (tttm) REVERT: F 117 MET cc_start: 0.7211 (mtp) cc_final: 0.6897 (mtp) REVERT: H 78 LYS cc_start: 0.6811 (pttp) cc_final: 0.6352 (pttm) REVERT: H 117 MET cc_start: 0.7166 (mtp) cc_final: 0.6795 (mtp) outliers start: 35 outliers final: 28 residues processed: 189 average time/residue: 0.4655 time to fit residues: 95.6682 Evaluate side-chains 193 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 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 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 5 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4705 r_free = 0.4705 target = 0.247029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.196741 restraints weight = 24435.055| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.37 r_work: 0.3804 rms_B_bonded: 4.26 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 = 0.32 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1236 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 : 0.441 7.333 14792 Z= 0.238 Chirality : 0.035 0.151 1672 Planarity : 0.003 0.040 1804 Dihedral : 3.939 57.260 1472 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.96 % Allowed : 22.13 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.23), residues: 1330 helix: 3.71 (0.16), residues: 954 sheet: 0.75 (1.28), residues: 20 loop : -0.71 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 65 TYR 0.011 0.001 TYR G 176 PHE 0.013 0.001 PHE E 180 TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00227 (10910) covalent geometry : angle 0.44122 (14776) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.29281 ( 16) hydrogen bonds : bond 0.04498 ( 850) hydrogen bonds : angle 3.28023 ( 2474) *********************** 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: 33 poor density : 171 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.4998 (pm20) REVERT: B 629 MET cc_start: 0.5982 (tpp) cc_final: 0.5374 (tpt) REVERT: D 566 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5011 (pm20) REVERT: E 24 MET cc_start: 0.3691 (tpt) cc_final: 0.2936 (tpt) REVERT: E 206 LYS cc_start: 0.6635 (ttmm) cc_final: 0.5871 (tttm) REVERT: G 113 ILE cc_start: 0.6611 (mt) cc_final: 0.6322 (mp) REVERT: G 206 LYS cc_start: 0.6681 (ttmm) cc_final: 0.5927 (tttm) REVERT: F 117 MET cc_start: 0.7104 (mtp) cc_final: 0.6783 (mtp) REVERT: H 78 LYS cc_start: 0.6736 (pttp) cc_final: 0.6351 (pttm) REVERT: H 117 MET cc_start: 0.7082 (mtp) cc_final: 0.6763 (mtp) outliers start: 33 outliers final: 28 residues processed: 192 average time/residue: 0.4850 time to fit residues: 101.3393 Evaluate side-chains 198 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 ARG 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 66 THR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 149 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.244939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.195012 restraints weight = 29990.812| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.49 r_work: 0.3777 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3761 r_free = 0.3761 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10918 Z= 0.148 Angle : 0.491 7.498 14792 Z= 0.266 Chirality : 0.036 0.141 1672 Planarity : 0.003 0.039 1804 Dihedral : 4.122 55.910 1472 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.23 % Allowed : 22.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.22), residues: 1330 helix: 3.49 (0.16), residues: 954 sheet: 0.80 (1.27), residues: 20 loop : -0.72 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.012 0.001 TYR E 181 PHE 0.019 0.002 PHE B 546 TRP 0.009 0.001 TRP B 578 HIS 0.003 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00309 (10910) covalent geometry : angle 0.49048 (14776) SS BOND : bond 0.00343 ( 8) SS BOND : angle 0.97930 ( 16) hydrogen bonds : bond 0.05251 ( 850) hydrogen bonds : angle 3.45711 ( 2474) *********************** 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 198 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.4997 (pm20) REVERT: B 629 MET cc_start: 0.5951 (tpp) cc_final: 0.5361 (tpt) REVERT: D 566 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: E 206 LYS cc_start: 0.6606 (ttmm) cc_final: 0.5842 (tttm) REVERT: G 206 LYS cc_start: 0.6649 (ttmm) cc_final: 0.5890 (tttm) REVERT: F 117 MET cc_start: 0.7240 (mtp) cc_final: 0.6929 (mtp) REVERT: H 78 LYS cc_start: 0.6812 (pttp) cc_final: 0.6346 (pttm) REVERT: H 117 MET cc_start: 0.7184 (mtp) cc_final: 0.6876 (mtp) REVERT: H 156 TYR cc_start: 0.8535 (t80) cc_final: 0.8310 (t80) outliers start: 36 outliers final: 29 residues processed: 185 average time/residue: 0.5218 time to fit residues: 104.8544 Evaluate side-chains 193 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 102 ARG 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 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 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4700 r_free = 0.4700 target = 0.246726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.196476 restraints weight = 28039.643| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.50 r_work: 0.3800 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1338 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= 0.120 Angle : 0.461 7.506 14792 Z= 0.247 Chirality : 0.035 0.149 1672 Planarity : 0.003 0.040 1804 Dihedral : 3.918 56.679 1472 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.05 % Allowed : 22.40 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.22), residues: 1330 helix: 3.66 (0.16), residues: 954 sheet: 0.89 (1.28), residues: 20 loop : -0.72 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 65 TYR 0.010 0.001 TYR G 181 PHE 0.018 0.001 PHE B 546 TRP 0.009 0.001 TRP E 178 HIS 0.002 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00239 (10910) covalent geometry : angle 0.46001 (14776) SS BOND : bond 0.00227 ( 8) SS BOND : angle 0.84901 ( 16) hydrogen bonds : bond 0.04607 ( 850) hydrogen bonds : angle 3.31786 ( 2474) *********************** 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 201 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.4997 (pm20) REVERT: B 629 MET cc_start: 0.5920 (tpp) cc_final: 0.5336 (tpt) REVERT: D 566 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.4982 (pm20) REVERT: E 24 MET cc_start: 0.3703 (tpt) cc_final: 0.2947 (tpt) REVERT: E 76 LEU cc_start: 0.5666 (tp) cc_final: 0.5258 (mt) REVERT: E 206 LYS cc_start: 0.6610 (ttmm) cc_final: 0.5839 (tttm) REVERT: G 24 MET cc_start: 0.3822 (tpt) cc_final: 0.2902 (tpt) REVERT: G 61 SER cc_start: 0.6234 (OUTLIER) cc_final: 0.5900 (p) REVERT: G 113 ILE cc_start: 0.6595 (mt) cc_final: 0.6326 (mp) REVERT: G 206 LYS cc_start: 0.6639 (ttmm) cc_final: 0.5882 (tttm) REVERT: F 117 MET cc_start: 0.7161 (mtp) cc_final: 0.6849 (mtp) REVERT: H 78 LYS cc_start: 0.6755 (pttp) cc_final: 0.6336 (pttm) REVERT: H 117 MET cc_start: 0.7091 (mtp) cc_final: 0.6784 (mtp) REVERT: H 156 TYR cc_start: 0.8520 (t80) cc_final: 0.8298 (t80) outliers start: 34 outliers final: 29 residues processed: 190 average time/residue: 0.5135 time to fit residues: 106.0683 Evaluate side-chains 196 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 102 ARG 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 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.246714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.208028 restraints weight = 22294.015| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 4.69 r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1376 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= 0.120 Angle : 0.461 7.554 14792 Z= 0.246 Chirality : 0.035 0.153 1672 Planarity : 0.003 0.040 1804 Dihedral : 3.868 56.754 1472 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.14 % Allowed : 21.86 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.22), residues: 1330 helix: 3.68 (0.16), residues: 954 sheet: 0.92 (1.28), residues: 20 loop : -0.70 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 65 TYR 0.010 0.001 TYR E 181 PHE 0.019 0.001 PHE B 546 TRP 0.009 0.001 TRP E 178 HIS 0.003 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00238 (10910) covalent geometry : angle 0.46066 (14776) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.79833 ( 16) hydrogen bonds : bond 0.04599 ( 850) hydrogen bonds : angle 3.30109 ( 2474) ********************** 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 196 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 566 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5073 (pm20) REVERT: B 629 MET cc_start: 0.6042 (tpp) cc_final: 0.5605 (tpt) REVERT: C 816 TYR cc_start: 0.6572 (t80) cc_final: 0.6258 (t80) REVERT: D 566 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5074 (pm20) REVERT: E 24 MET cc_start: 0.3948 (tpt) cc_final: 0.3236 (tpt) REVERT: E 76 LEU cc_start: 0.5503 (tp) cc_final: 0.5171 (mt) REVERT: E 131 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5053 (mtp180) REVERT: E 206 LYS cc_start: 0.7102 (ttmm) cc_final: 0.6467 (tttm) REVERT: G 24 MET cc_start: 0.4043 (tpt) cc_final: 0.3188 (tpt) REVERT: G 61 SER cc_start: 0.5917 (OUTLIER) cc_final: 0.5714 (p) REVERT: G 113 ILE cc_start: 0.6925 (mt) cc_final: 0.6682 (mp) REVERT: G 206 LYS cc_start: 0.7074 (ttmm) cc_final: 0.6466 (tttm) outliers start: 35 outliers final: 29 residues processed: 184 average time/residue: 0.5161 time to fit residues: 103.2159 Evaluate side-chains 194 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 102 ARG Chi-restraints excluded: chain E residue 131 ARG 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 31 ASP Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.246154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.208098 restraints weight = 21501.414| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 4.62 r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1404 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= 0.128 Angle : 0.471 7.571 14792 Z= 0.252 Chirality : 0.036 0.150 1672 Planarity : 0.003 0.040 1804 Dihedral : 3.903 56.446 1472 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.14 % Allowed : 22.04 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.22), residues: 1330 helix: 3.62 (0.16), residues: 954 sheet: 0.91 (1.26), residues: 20 loop : -0.72 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 65 TYR 0.010 0.001 TYR G 181 PHE 0.019 0.001 PHE B 546 TRP 0.008 0.001 TRP E 178 HIS 0.003 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00259 (10910) covalent geometry : angle 0.47023 (14776) SS BOND : bond 0.00225 ( 8) SS BOND : angle 0.78454 ( 16) hydrogen bonds : bond 0.04792 ( 850) hydrogen bonds : angle 3.35018 ( 2474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4561.72 seconds wall clock time: 78 minutes 9.52 seconds (4689.52 seconds total)