Starting phenix.real_space_refine on Tue May 13 17:09:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fp4_29359/05_2025/8fp4_29359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fp4_29359/05_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_29359/05_2025/8fp4_29359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fp4_29359/05_2025/8fp4_29359.map" model { file = "/net/cci-nas-00/data/ceres_data/8fp4_29359/05_2025/8fp4_29359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fp4_29359/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.43, per 1000 atoms: 0.96 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: 3.05 Conformation dependent library (CDL) restraints added in 2.2 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: 1.29 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 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: 3.56 Time building geometry restraints manager: 3.53 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: 2.700 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.300 Find NCS groups from input model: 0.560 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- 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 : 1.215 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: 1.0923 time to fit residues: 206.6764 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 : 1.221 ------------------------------------------------------------------------------- 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: 0.2784 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 : 1.185 Fit side-chains REVERT: B 619 ASN cc_start: 0.7304 (m-40) cc_final: 0.7101 (m-40) REVERT: E 26 ILE cc_start: 0.8398 (mm) cc_final: 0.8192 (mt) REVERT: G 26 ILE cc_start: 0.8366 (mm) cc_final: 0.8165 (mt) REVERT: H 122 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6948 (mm) REVERT: H 191 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8604 (mm-30) outliers start: 9 outliers final: 4 residues processed: 173 average time/residue: 1.0373 time to fit residues: 195.7216 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 : 1.133 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3851 r_free = 0.3851 target = 0.166131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123563 restraints weight = 25798.025| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.41 r_work: 0.2705 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10932 Z= 0.134 Angle : 0.443 6.897 14814 Z= 0.249 Chirality : 0.037 0.131 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.837 45.454 1469 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.61 % Allowed : 18.52 % Favored : 79.87 % 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: 4.12 (0.24), residues: 1336 helix: 3.71 (0.16), residues: 955 sheet: -0.49 (1.06), residues: 30 loop : 0.05 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.002 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 0.04805 ( 860) hydrogen bonds : angle 3.47118 ( 2498) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.65738 ( 16) covalent geometry : bond 0.00277 (10924) covalent geometry : angle 0.44249 (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 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.175 Fit side-chains REVERT: A 514 VAL cc_start: 0.7382 (m) cc_final: 0.7046 (p) REVERT: B 619 ASN cc_start: 0.7469 (m-40) cc_final: 0.7212 (m-40) REVERT: C 514 VAL cc_start: 0.7346 (m) cc_final: 0.7036 (p) REVERT: F 99 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6586 (tpp-160) REVERT: F 191 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8599 (mm-30) REVERT: H 122 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6982 (mm) REVERT: H 191 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8592 (mm-30) outliers start: 18 outliers final: 10 residues processed: 174 average time/residue: 1.1148 time to fit residues: 210.8576 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 : 1.118 ------------------------------------------------------------------------------- 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 G residue 175 SER Chi-restraints excluded: chain F residue 11 LEU 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: 10.0000 chunk 103 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.167741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113864 restraints weight = 35634.373| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.46 r_work: 0.2763 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 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 = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10932 Z= 0.112 Angle : 0.415 6.714 14814 Z= 0.231 Chirality : 0.035 0.132 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.630 32.347 1469 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 18.34 % 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: 956 sheet: 0.75 (1.48), residues: 20 loop : -0.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 178 HIS 0.003 0.001 HIS H 205 PHE 0.015 0.001 PHE E 127 TYR 0.010 0.001 TYR G 181 ARG 0.008 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 860) hydrogen bonds : angle 3.32706 ( 2498) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.62723 ( 16) covalent geometry : bond 0.00219 (10924) covalent geometry : angle 0.41440 (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 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.266 Fit side-chains REVERT: A 514 VAL cc_start: 0.7404 (m) cc_final: 0.7138 (p) REVERT: B 619 ASN cc_start: 0.7373 (m-40) cc_final: 0.7132 (m-40) REVERT: C 514 VAL cc_start: 0.7399 (m) cc_final: 0.7148 (p) REVERT: D 825 MET cc_start: 0.5404 (ppp) cc_final: 0.5049 (pp-130) REVERT: E 9 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: G 9 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: F 122 ILE cc_start: 0.7197 (mm) cc_final: 0.6980 (mm) REVERT: F 191 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8601 (mm-30) REVERT: H 122 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6941 (mm) REVERT: H 191 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8594 (mm-30) outliers start: 18 outliers final: 8 residues processed: 175 average time/residue: 1.1428 time to fit residues: 216.8131 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 9 GLN 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 209 ARG Chi-restraints excluded: chain F residue 203 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: 1.9990 chunk 78 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 149 ASN 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 = 0.3847 r_free = 0.3847 target = 0.165810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111653 restraints weight = 39192.656| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.36 r_work: 0.2734 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 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 = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10932 Z= 0.141 Angle : 0.452 6.418 14814 Z= 0.253 Chirality : 0.037 0.133 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.787 25.933 1469 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.97 % Allowed : 17.98 % 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: 4.07 (0.24), residues: 1336 helix: 3.67 (0.16), residues: 954 sheet: -0.35 (1.09), residues: 30 loop : 0.06 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS H 205 PHE 0.014 0.002 PHE E 127 TYR 0.014 0.002 TYR G 181 ARG 0.008 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 860) hydrogen bonds : angle 3.44088 ( 2498) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.71466 ( 16) covalent geometry : bond 0.00297 (10924) covalent geometry : angle 0.45209 (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 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.273 Fit side-chains REVERT: A 514 VAL cc_start: 0.7381 (m) cc_final: 0.7100 (p) REVERT: C 514 VAL cc_start: 0.7379 (m) cc_final: 0.7113 (p) REVERT: D 825 MET cc_start: 0.5400 (ppp) cc_final: 0.5052 (pp-130) REVERT: E 9 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: G 9 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: F 191 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8595 (mm-30) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 1.0905 time to fit residues: 211.4705 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 : 1.192 ------------------------------------------------------------------------------- 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 39 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 9 GLN 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 203 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125129 restraints weight = 29813.703| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.66 r_work: 0.2753 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10932 Z= 0.107 Angle : 0.409 5.854 14814 Z= 0.229 Chirality : 0.035 0.135 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.569 18.134 1469 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.43 % Allowed : 18.78 % 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: 4.22 (0.24), residues: 1336 helix: 3.78 (0.16), residues: 956 sheet: 0.47 (1.44), residues: 20 loop : 0.01 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 178 HIS 0.003 0.001 HIS H 205 PHE 0.013 0.001 PHE E 127 TYR 0.009 0.001 TYR G 181 ARG 0.008 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 860) hydrogen bonds : angle 3.29881 ( 2498) SS BOND : bond 0.00155 ( 8) SS BOND : angle 0.62759 ( 16) covalent geometry : bond 0.00206 (10924) covalent geometry : angle 0.40852 (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: 16 poor density : 164 time to evaluate : 1.259 Fit side-chains REVERT: A 514 VAL cc_start: 0.7370 (m) cc_final: 0.7068 (p) REVERT: B 619 ASN cc_start: 0.7416 (m-40) cc_final: 0.7186 (m-40) REVERT: C 514 VAL cc_start: 0.7374 (m) cc_final: 0.7091 (p) REVERT: D 825 MET cc_start: 0.5271 (ppp) cc_final: 0.4884 (pp-130) REVERT: F 99 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6658 (tpp-160) REVERT: F 191 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8581 (mm-30) outliers start: 16 outliers final: 11 residues processed: 175 average time/residue: 1.1217 time to fit residues: 213.3933 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 : 1.225 ------------------------------------------------------------------------------- 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 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 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112284 restraints weight = 36376.381| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.34 r_work: 0.2771 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 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 = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10932 Z= 0.132 Angle : 0.445 7.689 14814 Z= 0.248 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.035 1808 Dihedral : 3.678 17.758 1468 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 4.08 (0.24), residues: 1336 helix: 3.67 (0.16), residues: 955 sheet: -0.54 (1.03), residues: 30 loop : 0.09 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 606 HIS 0.003 0.001 HIS H 205 PHE 0.015 0.002 PHE E 127 TYR 0.013 0.001 TYR G 181 ARG 0.009 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 860) hydrogen bonds : angle 3.39463 ( 2498) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.69840 ( 16) covalent geometry : bond 0.00274 (10924) covalent geometry : angle 0.44427 (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 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.206 Fit side-chains REVERT: A 514 VAL cc_start: 0.7383 (m) cc_final: 0.7094 (p) REVERT: B 619 ASN cc_start: 0.7463 (m-40) cc_final: 0.7213 (m-40) REVERT: C 514 VAL cc_start: 0.7383 (m) cc_final: 0.7116 (p) REVERT: D 825 MET cc_start: 0.5242 (ppp) cc_final: 0.4895 (pp-130) REVERT: E 9 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6493 (tt0) REVERT: F 99 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6557 (tpp-160) outliers start: 16 outliers final: 13 residues processed: 171 average time/residue: 1.1271 time to fit residues: 209.1390 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 9 GLN 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 99 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109382 restraints weight = 34614.924| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.65 r_work: 0.2733 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 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 = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.003 0.024 10932 Z= 0.145 Angle : 0.461 7.461 14814 Z= 0.257 Chirality : 0.037 0.136 1674 Planarity : 0.003 0.036 1808 Dihedral : 3.773 18.282 1468 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.70 % Allowed : 18.34 % 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: 4.00 (0.24), residues: 1336 helix: 3.62 (0.16), residues: 954 sheet: -0.52 (1.02), residues: 30 loop : 0.04 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 606 HIS 0.004 0.001 HIS E 205 PHE 0.016 0.002 PHE E 127 TYR 0.015 0.002 TYR G 181 ARG 0.009 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 860) hydrogen bonds : angle 3.44345 ( 2498) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.77004 ( 16) covalent geometry : bond 0.00308 (10924) covalent geometry : angle 0.46097 (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 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.288 Fit side-chains REVERT: A 514 VAL cc_start: 0.7390 (m) cc_final: 0.7097 (p) REVERT: B 619 ASN cc_start: 0.7527 (m-40) cc_final: 0.7242 (m-40) REVERT: C 514 VAL cc_start: 0.7372 (m) cc_final: 0.7102 (p) REVERT: D 825 MET cc_start: 0.5232 (ppp) cc_final: 0.4890 (pp-130) REVERT: F 99 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6563 (tpp-160) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 1.1775 time to fit residues: 222.6719 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 99 ARG Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111910 restraints weight = 31939.379| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.49 r_work: 0.2752 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 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 = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10932 Z= 0.121 Angle : 0.429 6.727 14814 Z= 0.240 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.037 1808 Dihedral : 3.648 17.547 1468 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.25 % Allowed : 18.34 % Favored : 80.41 % 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: 4.10 (0.24), residues: 1336 helix: 3.68 (0.16), residues: 956 sheet: -0.46 (1.03), residues: 30 loop : 0.07 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 178 HIS 0.003 0.001 HIS H 205 PHE 0.016 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 0.04505 ( 860) hydrogen bonds : angle 3.37018 ( 2498) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.68154 ( 16) covalent geometry : bond 0.00243 (10924) covalent geometry : angle 0.42914 (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 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.140 Fit side-chains REVERT: A 514 VAL cc_start: 0.7363 (m) cc_final: 0.7087 (p) REVERT: B 619 ASN cc_start: 0.7421 (m-40) cc_final: 0.7163 (m-40) REVERT: C 514 VAL cc_start: 0.7334 (m) cc_final: 0.7074 (p) REVERT: D 825 MET cc_start: 0.5203 (ppp) cc_final: 0.4871 (pp-130) outliers start: 14 outliers final: 12 residues processed: 168 average time/residue: 1.1264 time to fit residues: 205.3048 Evaluate side-chains 165 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 14 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 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** F 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112824 restraints weight = 34328.929| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.37 r_work: 0.2759 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 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 = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10932 Z= 0.124 Angle : 0.435 6.789 14814 Z= 0.244 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.041 1808 Dihedral : 3.681 17.634 1468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.25 % Allowed : 18.52 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.24), residues: 1336 helix: 3.67 (0.16), residues: 955 sheet: -0.40 (1.04), residues: 30 loop : 0.06 (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 H 205 PHE 0.016 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 0.04558 ( 860) hydrogen bonds : angle 3.38496 ( 2498) SS BOND : bond 0.00219 ( 8) SS BOND : angle 0.69074 ( 16) covalent geometry : bond 0.00252 (10924) covalent geometry : angle 0.43472 (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 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.306 Fit side-chains REVERT: A 514 VAL cc_start: 0.7399 (m) cc_final: 0.7111 (p) REVERT: B 619 ASN cc_start: 0.7436 (m-40) cc_final: 0.7173 (m-40) REVERT: C 514 VAL cc_start: 0.7373 (m) cc_final: 0.7099 (p) REVERT: H 191 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8584 (mm-30) outliers start: 14 outliers final: 14 residues processed: 164 average time/residue: 1.1622 time to fit residues: 208.7444 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain E residue 14 THR 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: 0.9980 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 99 optimal weight: 0.0270 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS F 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 = 0.167263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124221 restraints weight = 30459.563| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.82 r_work: 0.2724 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10932 Z= 0.114 Angle : 0.422 6.527 14814 Z= 0.236 Chirality : 0.036 0.136 1674 Planarity : 0.003 0.040 1808 Dihedral : 3.609 17.224 1468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 4.15 (0.24), residues: 1336 helix: 3.73 (0.16), residues: 956 sheet: -0.38 (1.05), residues: 30 loop : 0.08 (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 H 205 PHE 0.015 0.001 PHE E 127 TYR 0.011 0.001 TYR G 181 ARG 0.010 0.000 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 860) hydrogen bonds : angle 3.33493 ( 2498) SS BOND : bond 0.00193 ( 8) SS BOND : angle 0.63830 ( 16) covalent geometry : bond 0.00226 (10924) covalent geometry : angle 0.42149 (14798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9620.52 seconds wall clock time: 165 minutes 55.18 seconds (9955.18 seconds total)