Starting phenix.real_space_refine on Mon Jul 28 22:50:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.map" model { file = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp4_29359/07_2025/8fp4_29359.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 Cl 2 4.86 5 C 7002 2.51 5 N 1708 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10876 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 149, 1165 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "B" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "C" Number of atoms: 1177 Number of conformers: 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 Conformer: "C" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Conformer: "A" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1183 Chain: "D" Number of atoms: 1233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1227 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 bond proxies already assigned to first conformer: 1253 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1467 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N BCYS C 589 " occ=0.38 ... (10 atoms not shown) pdb=" SG CCYS C 589 " occ=0.62 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 10.98, per 1000 atoms: 1.01 Number of scatterers: 10876 At special positions: 0 Unit cell: (112.34, 113.98, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 76 16.00 O 2088 8.00 N 1708 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 2.3 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 74.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 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 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 removed outlier: 3.552A pdb=" N LYS B 826 " --> pdb=" O ALA B 822 " (cutoff:3.500A) 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 624 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 624 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 84 through 89 removed outlier: 3.588A pdb=" N ASP E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.784A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.536A 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 84 through 89 removed outlier: 3.580A pdb=" N ASP G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.699A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 4.159A 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: 3.702A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 216 removed outlier: 3.570A 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: 4.015A 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: 3.661A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 216 removed outlier: 3.569A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AA2, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AA3, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 860 hydrogen bonds defined for protein. 2498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 3.47 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: 3232 1.34 - 1.46: 2910 1.46 - 1.58: 4666 1.58 - 1.70: 0 1.70 - 1.81: 116 Bond restraints: 10924 Sorted by residual: bond pdb=" CB MET D 825 " pdb=" CG MET D 825 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.61e-01 bond pdb=" C VAL A 792 " pdb=" O VAL A 792 " ideal model delta sigma weight residual 1.232 1.242 -0.010 1.30e-02 5.92e+03 5.94e-01 bond pdb=" N TYR E 128 " pdb=" CA TYR E 128 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.50e-02 4.44e+03 5.66e-01 bond pdb=" C ALA F 87 " pdb=" N ASP F 88 " ideal model delta sigma weight residual 1.328 1.337 -0.010 1.30e-02 5.92e+03 5.60e-01 bond pdb=" SD MET B 825 " pdb=" CE MET B 825 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 5.58e-01 ... (remaining 10919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14671 1.72 - 3.43: 106 3.43 - 5.15: 18 5.15 - 6.86: 2 6.86 - 8.58: 1 Bond angle restraints: 14798 Sorted by residual: angle pdb=" N VAL A 792 " pdb=" CA VAL A 792 " pdb=" C VAL A 792 " ideal model delta sigma weight residual 113.20 109.87 3.33 9.60e-01 1.09e+00 1.20e+01 angle pdb=" CA MET B 825 " pdb=" CB MET B 825 " pdb=" CG MET B 825 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.61e+00 angle pdb=" C ARG B 824 " pdb=" N MET B 825 " pdb=" CA MET B 825 " ideal model delta sigma weight residual 122.38 116.94 5.44 1.81e+00 3.05e-01 9.03e+00 angle pdb=" CB MET D 825 " pdb=" CG MET D 825 " pdb=" SD MET D 825 " ideal model delta sigma weight residual 112.70 121.28 -8.58 3.00e+00 1.11e-01 8.17e+00 angle pdb=" CA VAL A 792 " pdb=" C VAL A 792 " pdb=" N ALA A 793 " ideal model delta sigma weight residual 118.71 115.95 2.76 1.15e+00 7.56e-01 5.74e+00 ... (remaining 14793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5427 17.83 - 35.66: 591 35.66 - 53.49: 171 53.49 - 71.32: 29 71.32 - 89.15: 14 Dihedral angle restraints: 6232 sinusoidal: 2298 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASP D 590 " pdb=" CB ASP D 590 " pdb=" CG ASP D 590 " pdb=" OD1 ASP D 590 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 590 " pdb=" CB ASP B 590 " pdb=" CG ASP B 590 " pdb=" OD1 ASP B 590 " ideal model delta sinusoidal sigma weight residual -30.00 -86.55 56.55 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N GLY A 572 " pdb=" CA GLY A 572 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1048 0.026 - 0.052: 369 0.052 - 0.077: 187 0.077 - 0.103: 56 0.103 - 0.129: 14 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA VAL H 57 " pdb=" N VAL H 57 " pdb=" C VAL H 57 " pdb=" CB VAL H 57 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL F 57 " pdb=" N VAL F 57 " pdb=" C VAL F 57 " pdb=" CB VAL F 57 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA PHE E 107 " pdb=" N PHE E 107 " pdb=" C PHE E 107 " pdb=" CB PHE E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1671 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO E 108 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+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 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 107 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO F 108 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO F 108 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 108 " -0.015 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 450 2.72 - 3.27: 11097 3.27 - 3.81: 20457 3.81 - 4.36: 22553 4.36 - 4.90: 38664 Nonbonded interactions: 93221 Sorted by model distance: nonbonded pdb=" OE1 GLN D 586 " pdb=" O HOH D 901 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLN B 586 " pdb=" O HOH B 901 " model vdw 2.182 3.040 nonbonded pdb=" O HOH D 902 " pdb=" O HOH D 910 " model vdw 2.198 3.040 nonbonded pdb=" O HOH B 902 " pdb=" O HOH B 910 " model vdw 2.199 3.040 nonbonded pdb=" O HOH B 906 " pdb=" O HOH B 914 " model vdw 2.208 3.040 ... (remaining 93216 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: 0.03 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=0.38 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.720 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 0.024 10932 Z= 0.118 Angle : 0.422 8.576 14814 Z= 0.240 Chirality : 0.035 0.129 1674 Planarity : 0.003 0.033 1808 Dihedral : 16.680 89.147 3688 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 19.68 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.24), residues: 1336 helix: 3.74 (0.16), residues: 953 sheet: 0.35 (1.10), residues: 28 loop : 0.01 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.001 PHE E 127 TYR 0.011 0.001 TYR A 616 ARG 0.007 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.09919 ( 860) hydrogen bonds : angle 3.95304 ( 2498) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.53663 ( 16) covalent geometry : bond 0.00235 (10924) covalent geometry : angle 0.42220 (14798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.176 Fit side-chains REVERT: F 191 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8573 (mm-30) outliers start: 16 outliers final: 12 residues processed: 174 average time/residue: 1.2155 time to fit residues: 229.4628 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS F 149 ASN F 205 HIS H 149 ASN H 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.168291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113348 restraints weight = 32175.302| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.50 r_work: 0.2783 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10932 Z= 0.111 Angle : 0.410 7.461 14814 Z= 0.231 Chirality : 0.035 0.133 1674 Planarity : 0.003 0.033 1808 Dihedral : 4.142 53.187 1482 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.81 % Allowed : 19.77 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.24), residues: 1336 helix: 3.82 (0.16), residues: 956 sheet: 0.34 (1.15), residues: 28 loop : 0.03 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.001 PHE E 127 TYR 0.009 0.001 TYR G 181 ARG 0.005 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 860) hydrogen bonds : angle 3.41545 ( 2498) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.63769 ( 16) covalent geometry : bond 0.00212 (10924) covalent geometry : angle 0.41003 (14798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 1.167 Fit side-chains REVERT: B 619 ASN cc_start: 0.7304 (m-40) cc_final: 0.7103 (m-40) REVERT: E 26 ILE cc_start: 0.8396 (mm) cc_final: 0.8190 (mt) REVERT: G 26 ILE cc_start: 0.8364 (mm) cc_final: 0.8162 (mt) REVERT: H 122 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6941 (mm) REVERT: H 191 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8603 (mm-30) outliers start: 9 outliers final: 4 residues processed: 173 average time/residue: 1.1087 time to fit residues: 208.6792 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124819 restraints weight = 26270.578| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.48 r_work: 0.2734 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.114 Angle : 0.417 7.096 14814 Z= 0.234 Chirality : 0.036 0.132 1674 Planarity : 0.003 0.034 1808 Dihedral : 3.683 43.693 1469 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 18.69 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.24), residues: 1336 helix: 3.79 (0.16), residues: 956 sheet: -0.44 (1.07), residues: 30 loop : 0.08 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 178 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.001 PHE E 127 TYR 0.010 0.001 TYR G 181 ARG 0.008 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 860) hydrogen bonds : angle 3.37747 ( 2498) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.59548 ( 16) covalent geometry : bond 0.00225 (10924) covalent geometry : angle 0.41684 (14798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.085 Fit side-chains REVERT: A 514 VAL cc_start: 0.7375 (m) cc_final: 0.7059 (p) REVERT: B 619 ASN cc_start: 0.7428 (m-40) cc_final: 0.7185 (m-40) REVERT: C 514 VAL cc_start: 0.7361 (m) cc_final: 0.7071 (p) REVERT: E 26 ILE cc_start: 0.8379 (mm) cc_final: 0.8174 (mt) REVERT: G 26 ILE cc_start: 0.8361 (mm) cc_final: 0.8161 (mt) REVERT: F 99 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6622 (tpp-160) REVERT: F 191 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8604 (mm-30) REVERT: H 122 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6954 (mm) REVERT: H 191 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8593 (mm-30) outliers start: 17 outliers final: 8 residues processed: 179 average time/residue: 1.1707 time to fit residues: 228.3496 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS F 149 ASN H 149 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111160 restraints weight = 35554.748| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.71 r_work: 0.2760 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10932 Z= 0.121 Angle : 0.429 8.070 14814 Z= 0.239 Chirality : 0.036 0.131 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.660 30.774 1469 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 18.60 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.24), residues: 1336 helix: 3.78 (0.16), residues: 955 sheet: 0.77 (1.49), residues: 20 loop : -0.00 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 178 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.001 PHE E 127 TYR 0.011 0.001 TYR G 181 ARG 0.008 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 860) hydrogen bonds : angle 3.36964 ( 2498) SS BOND : bond 0.00233 ( 8) SS BOND : angle 0.66697 ( 16) covalent geometry : bond 0.00243 (10924) covalent geometry : angle 0.42915 (14798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.312 Fit side-chains REVERT: A 514 VAL cc_start: 0.7389 (m) cc_final: 0.7110 (p) REVERT: B 619 ASN cc_start: 0.7406 (m-40) cc_final: 0.7155 (m-40) REVERT: C 514 VAL cc_start: 0.7342 (m) cc_final: 0.7088 (p) REVERT: D 825 MET cc_start: 0.5423 (ppp) cc_final: 0.5060 (pp-130) REVERT: G 9 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: F 191 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8599 (mm-30) REVERT: H 122 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6964 (mm) REVERT: H 191 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8589 (mm-30) outliers start: 15 outliers final: 10 residues processed: 176 average time/residue: 1.2143 time to fit residues: 231.6132 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 122 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 149 ASN F 149 ASN H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110706 restraints weight = 39950.264| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.72 r_work: 0.2745 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10932 Z= 0.123 Angle : 0.430 7.620 14814 Z= 0.240 Chirality : 0.036 0.134 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.642 20.420 1469 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 18.16 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.24), residues: 1336 helix: 3.76 (0.16), residues: 955 sheet: 0.69 (1.47), residues: 20 loop : 0.00 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 178 HIS 0.003 0.001 HIS F 205 PHE 0.014 0.001 PHE E 127 TYR 0.012 0.001 TYR G 181 ARG 0.008 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 860) hydrogen bonds : angle 3.36653 ( 2498) SS BOND : bond 0.00228 ( 8) SS BOND : angle 0.65676 ( 16) covalent geometry : bond 0.00249 (10924) covalent geometry : angle 0.42967 (14798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.659 Fit side-chains REVERT: A 514 VAL cc_start: 0.7380 (m) cc_final: 0.7081 (p) REVERT: B 619 ASN cc_start: 0.7427 (m-40) cc_final: 0.7162 (m-40) REVERT: C 514 VAL cc_start: 0.7314 (m) cc_final: 0.7045 (p) REVERT: D 825 MET cc_start: 0.5287 (ppp) cc_final: 0.4867 (pp-130) REVERT: E 9 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: G 9 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6539 (tt0) REVERT: F 191 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8590 (mm-30) REVERT: H 191 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8574 (mm-30) outliers start: 21 outliers final: 11 residues processed: 174 average time/residue: 1.3892 time to fit residues: 262.2434 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123251 restraints weight = 29734.327| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.82 r_work: 0.2736 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10932 Z= 0.121 Angle : 0.427 5.751 14814 Z= 0.240 Chirality : 0.036 0.134 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.621 17.463 1468 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.79 % Allowed : 18.25 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.24), residues: 1336 helix: 3.74 (0.16), residues: 955 sheet: -0.48 (1.05), residues: 30 loop : 0.10 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 178 HIS 0.003 0.001 HIS F 205 PHE 0.013 0.001 PHE E 127 TYR 0.011 0.001 TYR G 181 ARG 0.009 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 860) hydrogen bonds : angle 3.35323 ( 2498) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.66736 ( 16) covalent geometry : bond 0.00245 (10924) covalent geometry : angle 0.42642 (14798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.178 Fit side-chains REVERT: A 514 VAL cc_start: 0.7425 (m) cc_final: 0.7083 (p) REVERT: B 619 ASN cc_start: 0.7483 (m-40) cc_final: 0.7211 (m-40) REVERT: C 514 VAL cc_start: 0.7413 (m) cc_final: 0.7095 (p) REVERT: D 825 MET cc_start: 0.5269 (ppp) cc_final: 0.4878 (pp-130) REVERT: F 191 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8581 (mm-30) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 1.1831 time to fit residues: 223.6730 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111972 restraints weight = 37525.590| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.62 r_work: 0.2770 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10932 Z= 0.117 Angle : 0.423 7.163 14814 Z= 0.237 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.573 17.320 1468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.25 % Allowed : 18.60 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.24), residues: 1336 helix: 3.77 (0.16), residues: 956 sheet: -0.58 (1.04), residues: 30 loop : 0.11 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 178 HIS 0.003 0.001 HIS F 205 PHE 0.015 0.001 PHE E 127 TYR 0.011 0.001 TYR G 181 ARG 0.009 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 860) hydrogen bonds : angle 3.33133 ( 2498) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.64572 ( 16) covalent geometry : bond 0.00234 (10924) covalent geometry : angle 0.42268 (14798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.106 Fit side-chains REVERT: A 514 VAL cc_start: 0.7400 (m) cc_final: 0.7109 (p) REVERT: B 619 ASN cc_start: 0.7424 (m-40) cc_final: 0.7168 (m-40) REVERT: C 514 VAL cc_start: 0.7390 (m) cc_final: 0.7119 (p) REVERT: F 191 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8590 (mm-30) REVERT: H 191 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8583 (mm-30) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 1.3093 time to fit residues: 243.2645 Evaluate side-chains 166 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 203 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113519 restraints weight = 35777.328| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.31 r_work: 0.2783 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.120 Angle : 0.428 7.475 14814 Z= 0.239 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.037 1808 Dihedral : 3.597 17.466 1468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.34 % Allowed : 18.60 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.24), residues: 1336 helix: 3.76 (0.16), residues: 955 sheet: -0.53 (1.03), residues: 30 loop : 0.10 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 178 HIS 0.003 0.001 HIS F 205 PHE 0.015 0.001 PHE E 127 TYR 0.011 0.001 TYR G 181 ARG 0.009 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 860) hydrogen bonds : angle 3.34502 ( 2498) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.68445 ( 16) covalent geometry : bond 0.00242 (10924) covalent geometry : angle 0.42741 (14798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.240 Fit side-chains REVERT: A 514 VAL cc_start: 0.7389 (m) cc_final: 0.7106 (p) REVERT: B 619 ASN cc_start: 0.7434 (m-40) cc_final: 0.7146 (m-40) REVERT: C 514 VAL cc_start: 0.7375 (m) cc_final: 0.7108 (p) REVERT: F 191 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8589 (mm-30) outliers start: 15 outliers final: 12 residues processed: 169 average time/residue: 1.5895 time to fit residues: 290.5241 Evaluate side-chains 167 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.166795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112167 restraints weight = 31944.656| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.45 r_work: 0.2767 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.122 Angle : 0.431 7.379 14814 Z= 0.241 Chirality : 0.036 0.137 1674 Planarity : 0.003 0.039 1808 Dihedral : 3.614 17.537 1468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 18.69 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.24), residues: 1336 helix: 3.74 (0.16), residues: 955 sheet: -0.51 (1.04), residues: 30 loop : 0.08 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 178 HIS 0.003 0.001 HIS F 205 PHE 0.015 0.001 PHE E 127 TYR 0.012 0.001 TYR G 181 ARG 0.010 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 860) hydrogen bonds : angle 3.34976 ( 2498) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.67765 ( 16) covalent geometry : bond 0.00248 (10924) covalent geometry : angle 0.43045 (14798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.613 Fit side-chains REVERT: A 514 VAL cc_start: 0.7405 (m) cc_final: 0.7113 (p) REVERT: B 619 ASN cc_start: 0.7422 (m-40) cc_final: 0.7162 (m-40) REVERT: C 514 VAL cc_start: 0.7391 (m) cc_final: 0.7124 (p) REVERT: F 191 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8585 (mm-30) outliers start: 15 outliers final: 13 residues processed: 169 average time/residue: 1.9023 time to fit residues: 349.3079 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.113895 restraints weight = 34509.775| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.36 r_work: 0.2764 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.115 Angle : 0.423 7.343 14814 Z= 0.236 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.040 1808 Dihedral : 3.571 17.211 1468 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.43 % Allowed : 18.52 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.24), residues: 1336 helix: 3.77 (0.16), residues: 956 sheet: -0.46 (1.04), residues: 30 loop : 0.09 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 178 HIS 0.003 0.001 HIS F 205 PHE 0.015 0.001 PHE E 127 TYR 0.011 0.001 TYR E 35 ARG 0.010 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 860) hydrogen bonds : angle 3.32501 ( 2498) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.64630 ( 16) covalent geometry : bond 0.00227 (10924) covalent geometry : angle 0.42317 (14798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.599 Fit side-chains REVERT: A 514 VAL cc_start: 0.7365 (m) cc_final: 0.7085 (p) REVERT: B 619 ASN cc_start: 0.7417 (m-40) cc_final: 0.7151 (m-40) REVERT: C 514 VAL cc_start: 0.7354 (m) cc_final: 0.7094 (p) REVERT: F 191 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8596 (mm-30) REVERT: H 191 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8588 (mm-30) outliers start: 16 outliers final: 14 residues processed: 166 average time/residue: 2.0049 time to fit residues: 361.6240 Evaluate side-chains 170 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 89 TYR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 99 optimal weight: 0.0570 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN H 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.167324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123630 restraints weight = 30527.094| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.89 r_work: 0.2739 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10932 Z= 0.114 Angle : 0.422 7.335 14814 Z= 0.236 Chirality : 0.035 0.136 1674 Planarity : 0.003 0.041 1808 Dihedral : 3.563 17.114 1468 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 18.60 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.24), residues: 1336 helix: 3.77 (0.16), residues: 956 sheet: -0.41 (1.05), residues: 30 loop : 0.10 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 178 HIS 0.003 0.001 HIS F 205 PHE 0.015 0.001 PHE E 127 TYR 0.012 0.001 TYR E 35 ARG 0.010 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 860) hydrogen bonds : angle 3.31990 ( 2498) SS BOND : bond 0.00184 ( 8) SS BOND : angle 0.64032 ( 16) covalent geometry : bond 0.00226 (10924) covalent geometry : angle 0.42194 (14798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11531.96 seconds wall clock time: 211 minutes 14.38 seconds (12674.38 seconds total)