Starting phenix.real_space_refine on Mon Jun 9 07:25:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.map" model { file = "/net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ity_60883/06_2025/9ity_60883.cif" } resolution = 4.95 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= 0.008 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 6573 2.51 5 N 1907 2.21 5 O 1977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10477 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 763 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 289 Chain: "V" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 762 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 292 Chain: "X" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 757 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 2, 'TRANS': 149} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 292 Chain: "U" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 766 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 289 Chain: "H" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "I" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 490 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "M" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 502 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Z" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1280 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 809 Unresolved non-hydrogen angles: 1058 Unresolved non-hydrogen dihedrals: 681 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 34, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 416 Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1104 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 709 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 30, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 9.48, per 1000 atoms: 0.90 Number of scatterers: 10477 At special positions: 0 Unit cell: (84.63, 140.43, 225.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1977 8.00 N 1907 7.00 C 6573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 1 sheets defined 87.3% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'Y' and resid 8 through 29 removed outlier: 4.194A pdb=" N ILE Y 12 " --> pdb=" O PRO Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 146 removed outlier: 3.742A pdb=" N ALA Y 146 " --> pdb=" O ALA Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 158 removed outlier: 3.567A pdb=" N GLU Y 155 " --> pdb=" O ALA Y 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 28 removed outlier: 3.737A pdb=" N PHE V 11 " --> pdb=" O ASN V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 120 Processing helix chain 'V' and resid 121 through 139 removed outlier: 4.083A pdb=" N LYS V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE V 128 " --> pdb=" O ALA V 124 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA V 129 " --> pdb=" O LYS V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 156 Processing helix chain 'X' and resid 7 through 123 removed outlier: 4.607A pdb=" N ARG X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Proline residue: X 32 - end of helix removed outlier: 4.565A pdb=" N ARG X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE X 44 " --> pdb=" O ARG X 40 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU X 45 " --> pdb=" O THR X 41 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 135 removed outlier: 4.282A pdb=" N GLN X 127 " --> pdb=" O GLU X 123 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 156 removed outlier: 4.398A pdb=" N ILE X 153 " --> pdb=" O HIS X 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 148 removed outlier: 3.661A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 4.746A pdb=" N ARG U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY U 141 " --> pdb=" O SER U 137 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA U 142 " --> pdb=" O ARG U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 160 removed outlier: 3.685A pdb=" N ILE U 153 " --> pdb=" O HIS U 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU U 160 " --> pdb=" O SER U 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 17 removed outlier: 3.618A pdb=" N ALA H 12 " --> pdb=" O ALA H 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 17 " --> pdb=" O VAL H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 38 removed outlier: 4.104A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 61 removed outlier: 3.659A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA H 54 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 3.606A pdb=" N ILE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.104A pdb=" N ALA I 12 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.590A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 71 removed outlier: 3.921A pdb=" N THR I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY I 52 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE I 53 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 17 removed outlier: 3.805A pdb=" N ALA J 17 " --> pdb=" O VAL J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 38 Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.722A pdb=" N THR J 47 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA J 58 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 10 removed outlier: 3.579A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 10 " --> pdb=" O LEU K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.803A pdb=" N GLY K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA K 17 " --> pdb=" O VAL K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 36 removed outlier: 3.550A pdb=" N ILE K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 70 removed outlier: 4.365A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY K 52 " --> pdb=" O TYR K 48 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE K 53 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 17 removed outlier: 3.584A pdb=" N ALA L 10 " --> pdb=" O LEU L 6 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA L 12 " --> pdb=" O ALA L 8 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL L 13 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA L 17 " --> pdb=" O VAL L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 38 removed outlier: 4.586A pdb=" N GLY L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 61 removed outlier: 3.821A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU L 59 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 69 removed outlier: 3.513A pdb=" N VAL L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE L 68 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 17 removed outlier: 4.342A pdb=" N ALA M 12 " --> pdb=" O ALA M 8 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL M 13 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 4.384A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 58 removed outlier: 3.639A pdb=" N ALA M 58 " --> pdb=" O ALA M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.675A pdb=" N VAL M 65 " --> pdb=" O ILE M 61 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 36 removed outlier: 3.692A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 61 removed outlier: 4.250A pdb=" N THR N 47 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 71 removed outlier: 4.065A pdb=" N VAL N 65 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE N 68 " --> pdb=" O LEU N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.509A pdb=" N ALA O 10 " --> pdb=" O LEU O 6 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA O 12 " --> pdb=" O ALA O 8 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA O 17 " --> pdb=" O VAL O 13 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix removed outlier: 4.778A pdb=" N GLY O 25 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 71 removed outlier: 3.554A pdb=" N PHE O 55 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA O 58 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE O 66 " --> pdb=" O PHE O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 10 Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.111A pdb=" N GLY P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 38 removed outlier: 4.738A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.543A pdb=" N VAL P 46 " --> pdb=" O GLU P 42 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY P 52 " --> pdb=" O TYR P 48 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE P 53 " --> pdb=" O MET P 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU P 59 " --> pdb=" O PHE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 66 through 72 removed outlier: 3.953A pdb=" N ILE P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.626A pdb=" N LEU Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA Q 12 " --> pdb=" O ALA Q 8 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL Q 13 " --> pdb=" O THR Q 9 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA Q 17 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE Q 18 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.574A pdb=" N GLY Q 25 " --> pdb=" O GLY Q 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 60 removed outlier: 3.528A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 71 removed outlier: 3.627A pdb=" N VAL Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE Q 68 " --> pdb=" O LEU Q 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.983A pdb=" N SER Z 21 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG Z 22 " --> pdb=" O ILE Z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 18 through 22' Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 79 through 99 Processing helix chain 'Z' and resid 106 through 126 Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 212 Processing helix chain 'Z' and resid 217 through 222 Processing helix chain 'Z' and resid 227 through 268 Proline residue: Z 243 - end of helix removed outlier: 3.542A pdb=" N ALA Z 247 " --> pdb=" O PRO Z 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU Z 258 " --> pdb=" O ILE Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 3.596A pdb=" N PHE Z 279 " --> pdb=" O PRO Z 275 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA Z 292 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 54 Processing helix chain 'T' and resid 56 through 72 removed outlier: 4.117A pdb=" N PHE T 61 " --> pdb=" O ILE T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 99 Processing helix chain 'T' and resid 106 through 125 removed outlier: 4.465A pdb=" N THR T 112 " --> pdb=" O PRO T 108 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE T 113 " --> pdb=" O LEU T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 213 removed outlier: 3.616A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 217 Processing helix chain 'T' and resid 229 through 262 removed outlier: 3.608A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) Proline residue: T 243 - end of helix removed outlier: 3.934A pdb=" N VAL T 262 " --> pdb=" O GLU T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 262 through 268 removed outlier: 3.649A pdb=" N PHE T 266 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU T 267 " --> pdb=" O VAL T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 303 removed outlier: 4.518A pdb=" N GLY T 278 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE T 279 " --> pdb=" O PRO T 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 133 through 134 1143 hydrogen bonds defined for protein. 3417 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: 5.34 Time building geometry restraints manager: 4.13 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: 3816 1.34 - 1.46: 912 1.46 - 1.57: 5764 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 10532 Sorted by residual: bond pdb=" N ILE T 301 " pdb=" CA ILE T 301 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.72e+00 bond pdb=" N ASN T 300 " pdb=" CA ASN T 300 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.27e+00 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.65e+00 bond pdb=" N ALA T 302 " pdb=" CA ALA T 302 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.30e+00 bond pdb=" N PHE K 72 " pdb=" CA PHE K 72 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.10e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 14112 1.23 - 2.46: 309 2.46 - 3.69: 51 3.69 - 4.93: 14 4.93 - 6.16: 4 Bond angle restraints: 14490 Sorted by residual: angle pdb=" N ILE M 41 " pdb=" CA ILE M 41 " pdb=" C ILE M 41 " ideal model delta sigma weight residual 111.91 108.33 3.58 8.90e-01 1.26e+00 1.62e+01 angle pdb=" N ILE N 61 " pdb=" CA ILE N 61 " pdb=" C ILE N 61 " ideal model delta sigma weight residual 111.91 108.45 3.46 8.90e-01 1.26e+00 1.51e+01 angle pdb=" N ILE K 41 " pdb=" CA ILE K 41 " pdb=" C ILE K 41 " ideal model delta sigma weight residual 112.98 108.98 4.00 1.25e+00 6.40e-01 1.03e+01 angle pdb=" C LYS T 178 " pdb=" N LYS T 179 " pdb=" CA LYS T 179 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.23e+00 angle pdb=" N ILE P 41 " pdb=" CA ILE P 41 " pdb=" C ILE P 41 " ideal model delta sigma weight residual 112.98 109.31 3.67 1.25e+00 6.40e-01 8.64e+00 ... (remaining 14485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 5808 16.23 - 32.45: 257 32.45 - 48.67: 23 48.67 - 64.90: 7 64.90 - 81.12: 2 Dihedral angle restraints: 6097 sinusoidal: 1016 harmonic: 5081 Sorted by residual: dihedral pdb=" CA PHE P 68 " pdb=" C PHE P 68 " pdb=" N LEU P 69 " pdb=" CA LEU P 69 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LEU T 270 " pdb=" C LEU T 270 " pdb=" N LEU T 271 " pdb=" CA LEU T 271 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA PHE J 55 " pdb=" C PHE J 55 " pdb=" N THR J 56 " pdb=" CA THR J 56 " ideal model delta harmonic sigma weight residual 180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1662 0.062 - 0.123: 259 0.123 - 0.185: 7 0.185 - 0.247: 2 0.247 - 0.309: 1 Chirality restraints: 1931 Sorted by residual: chirality pdb=" CB ILE O 41 " pdb=" CA ILE O 41 " pdb=" CG1 ILE O 41 " pdb=" CG2 ILE O 41 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" CG1 ILE Q 41 " pdb=" CG2 ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE T 301 " pdb=" N ILE T 301 " pdb=" C ILE T 301 " pdb=" CB ILE T 301 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1928 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 19 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO J 20 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO J 20 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO J 20 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN N 38 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO N 39 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO N 39 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 39 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 19 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO H 20 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 20 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 20 " -0.032 5.00e-02 4.00e+02 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2008 2.76 - 3.29: 11981 3.29 - 3.83: 19251 3.83 - 4.36: 20496 4.36 - 4.90: 32502 Nonbonded interactions: 86238 Sorted by model distance: nonbonded pdb=" O LEU O 6 " pdb=" OG1 THR O 9 " model vdw 2.223 3.040 nonbonded pdb=" NH1 ARG H 37 " pdb=" OE1 GLN I 33 " model vdw 2.244 3.120 nonbonded pdb=" NE2 GLN H 33 " pdb=" O GLY Q 30 " model vdw 2.278 3.120 nonbonded pdb=" O GLN J 33 " pdb=" NE ARG J 37 " model vdw 2.285 3.120 nonbonded pdb=" O ASN N 5 " pdb=" OG1 THR N 9 " model vdw 2.287 3.040 ... (remaining 86233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and resid 1 through 69) selection = (chain 'I' and resid 1 through 69) selection = (chain 'J' and resid 1 through 69) selection = (chain 'K' and resid 1 through 69) selection = chain 'L' selection = (chain 'M' and resid 1 through 69) selection = (chain 'N' and resid 1 through 69) selection = (chain 'O' and resid 1 through 69) selection = (chain 'P' and resid 1 through 69) selection = (chain 'Q' and resid 1 through 69) } ncs_group { reference = (chain 'T' and (resid 47 through 135 or resid 170 through 303)) selection = (chain 'Z' and (resid 47 through 135 or resid 170 through 303)) } ncs_group { reference = (chain 'U' and resid 8 through 156) selection = (chain 'V' and resid 8 through 156) selection = (chain 'X' and resid 8 through 156) selection = (chain 'Y' and resid 8 through 156) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 230.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.350 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4681 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 0.036 10532 Z= 0.135 Angle : 0.480 6.157 14490 Z= 0.296 Chirality : 0.040 0.309 1931 Planarity : 0.004 0.066 1962 Dihedral : 10.210 81.125 2815 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.81 (0.20), residues: 1771 helix: 2.31 (0.14), residues: 1253 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.008 0.001 PHE P 62 TYR 0.005 0.001 TYR H 48 ARG 0.002 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.24063 ( 1143) hydrogen bonds : angle 6.06046 ( 3417) covalent geometry : bond 0.00228 (10532) covalent geometry : angle 0.48006 (14490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9422 (mt) cc_final: 0.8921 (mt) REVERT: K 41 ILE cc_start: 0.8624 (tp) cc_final: 0.8414 (pt) REVERT: K 43 ASN cc_start: 0.8526 (p0) cc_final: 0.8081 (m-40) REVERT: K 45 VAL cc_start: 0.9187 (t) cc_final: 0.8889 (p) REVERT: K 59 LEU cc_start: 0.4878 (mt) cc_final: 0.4551 (mt) REVERT: L 24 ILE cc_start: 0.9232 (mt) cc_final: 0.8984 (pt) REVERT: L 27 ILE cc_start: 0.9488 (mt) cc_final: 0.9012 (mt) REVERT: O 27 ILE cc_start: 0.9599 (mt) cc_final: 0.9372 (mt) REVERT: P 70 ILE cc_start: 0.4622 (mm) cc_final: 0.4282 (mt) REVERT: Q 27 ILE cc_start: 0.9556 (mt) cc_final: 0.9231 (mt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1690 time to fit residues: 58.9751 Evaluate side-chains 156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 160 optimal weight: 0.2980 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN K 33 GLN N 33 GLN ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.036257 restraints weight = 113958.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036474 restraints weight = 101819.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036611 restraints weight = 95119.274| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10532 Z= 0.246 Angle : 0.590 8.419 14490 Z= 0.354 Chirality : 0.041 0.204 1931 Planarity : 0.006 0.071 1962 Dihedral : 4.343 18.408 1819 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.20 % Allowed : 4.87 % Favored : 94.93 % 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: 1.58 (0.20), residues: 1771 helix: 1.73 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.035 0.002 PHE H 62 TYR 0.013 0.001 TYR K 48 ARG 0.008 0.001 ARG O 37 Details of bonding type rmsd hydrogen bonds : bond 0.05975 ( 1143) hydrogen bonds : angle 4.53010 ( 3417) covalent geometry : bond 0.00410 (10532) covalent geometry : angle 0.58956 (14490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9474 (mt) cc_final: 0.9171 (mt) REVERT: K 41 ILE cc_start: 0.9137 (tp) cc_final: 0.8804 (tp) REVERT: K 43 ASN cc_start: 0.9226 (p0) cc_final: 0.9016 (m-40) REVERT: L 49 MET cc_start: 0.9067 (tmm) cc_final: 0.8695 (mmt) REVERT: O 15 LEU cc_start: 0.9746 (mp) cc_final: 0.9525 (mp) REVERT: P 70 ILE cc_start: 0.6946 (mm) cc_final: 0.6663 (mt) REVERT: Q 24 ILE cc_start: 0.9373 (mt) cc_final: 0.9083 (pt) REVERT: Q 32 VAL cc_start: 0.9516 (p) cc_final: 0.9289 (p) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1664 time to fit residues: 47.9429 Evaluate side-chains 130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 48 optimal weight: 80.0000 chunk 158 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.036253 restraints weight = 113430.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.036423 restraints weight = 101296.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036542 restraints weight = 95152.077| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10532 Z= 0.181 Angle : 0.532 7.649 14490 Z= 0.309 Chirality : 0.040 0.213 1931 Planarity : 0.005 0.075 1962 Dihedral : 4.134 17.236 1819 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 1.74 (0.20), residues: 1771 helix: 1.80 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.022 0.002 PHE Q 55 TYR 0.009 0.001 TYR H 48 ARG 0.004 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 1143) hydrogen bonds : angle 4.13610 ( 3417) covalent geometry : bond 0.00325 (10532) covalent geometry : angle 0.53200 (14490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9210 (mt) cc_final: 0.8770 (mt) REVERT: K 24 ILE cc_start: 0.8899 (mt) cc_final: 0.8607 (pt) REVERT: K 41 ILE cc_start: 0.8840 (tp) cc_final: 0.8569 (tp) REVERT: K 43 ASN cc_start: 0.9083 (p0) cc_final: 0.8855 (m-40) REVERT: L 4 LEU cc_start: 0.9458 (mt) cc_final: 0.9186 (mt) REVERT: M 27 ILE cc_start: 0.9209 (mt) cc_final: 0.8917 (mt) REVERT: O 27 ILE cc_start: 0.9684 (mt) cc_final: 0.9481 (mt) REVERT: P 70 ILE cc_start: 0.5228 (mm) cc_final: 0.5004 (mt) REVERT: Q 24 ILE cc_start: 0.8960 (mt) cc_final: 0.8726 (mt) REVERT: Q 53 ILE cc_start: 0.5200 (mt) cc_final: 0.4643 (mt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1776 time to fit residues: 50.0717 Evaluate side-chains 135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 152 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN Q 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.036368 restraints weight = 112603.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036467 restraints weight = 105110.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036467 restraints weight = 99935.664| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10532 Z= 0.174 Angle : 0.509 7.187 14490 Z= 0.301 Chirality : 0.040 0.196 1931 Planarity : 0.005 0.078 1962 Dihedral : 4.089 16.190 1819 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1771 helix: 1.89 (0.13), residues: 1418 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.019 0.001 PHE O 55 TYR 0.009 0.001 TYR K 48 ARG 0.005 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1143) hydrogen bonds : angle 3.99172 ( 3417) covalent geometry : bond 0.00314 (10532) covalent geometry : angle 0.50879 (14490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9361 (mt) cc_final: 0.9156 (mt) REVERT: J 59 LEU cc_start: 0.6107 (mt) cc_final: 0.5782 (mt) REVERT: K 24 ILE cc_start: 0.9270 (mt) cc_final: 0.8947 (pt) REVERT: K 41 ILE cc_start: 0.9179 (tp) cc_final: 0.8830 (tp) REVERT: K 43 ASN cc_start: 0.9188 (p0) cc_final: 0.8884 (m-40) REVERT: K 56 THR cc_start: 0.9070 (p) cc_final: 0.8759 (t) REVERT: L 4 LEU cc_start: 0.9545 (mt) cc_final: 0.9261 (mt) REVERT: L 27 ILE cc_start: 0.9705 (mt) cc_final: 0.9440 (pt) REVERT: L 57 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8945 (mp0) REVERT: M 27 ILE cc_start: 0.9624 (mt) cc_final: 0.9295 (mt) REVERT: P 27 ILE cc_start: 0.9708 (mm) cc_final: 0.9506 (mm) REVERT: P 53 ILE cc_start: 0.6783 (mt) cc_final: 0.6499 (mt) REVERT: P 70 ILE cc_start: 0.7001 (mm) cc_final: 0.6722 (mt) REVERT: Q 24 ILE cc_start: 0.9355 (mt) cc_final: 0.9116 (mt) REVERT: Q 27 ILE cc_start: 0.9124 (mt) cc_final: 0.8504 (mt) REVERT: Q 53 ILE cc_start: 0.6411 (mt) cc_final: 0.6195 (mt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1706 time to fit residues: 46.8706 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 168 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 141 optimal weight: 50.0000 chunk 68 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035744 restraints weight = 110440.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035892 restraints weight = 100251.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.036033 restraints weight = 95114.491| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10532 Z= 0.143 Angle : 0.484 5.931 14490 Z= 0.281 Chirality : 0.040 0.188 1931 Planarity : 0.005 0.077 1962 Dihedral : 3.912 15.537 1819 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 2.22 (0.20), residues: 1771 helix: 2.18 (0.13), residues: 1417 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.027 0.001 PHE Q 50 TYR 0.011 0.001 TYR J 48 ARG 0.003 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 1143) hydrogen bonds : angle 3.68789 ( 3417) covalent geometry : bond 0.00266 (10532) covalent geometry : angle 0.48414 (14490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9125 (mt) cc_final: 0.8822 (mt) REVERT: J 59 LEU cc_start: 0.5077 (mt) cc_final: 0.4808 (mt) REVERT: J 68 PHE cc_start: 0.8726 (m-10) cc_final: 0.8499 (m-80) REVERT: K 24 ILE cc_start: 0.9110 (mt) cc_final: 0.8775 (pt) REVERT: K 41 ILE cc_start: 0.8876 (tp) cc_final: 0.8526 (tp) REVERT: K 43 ASN cc_start: 0.9101 (p0) cc_final: 0.8786 (m-40) REVERT: K 56 THR cc_start: 0.7436 (p) cc_final: 0.7002 (t) REVERT: P 27 ILE cc_start: 0.9707 (mm) cc_final: 0.9502 (mm) REVERT: P 70 ILE cc_start: 0.5908 (mm) cc_final: 0.5637 (mt) REVERT: Q 24 ILE cc_start: 0.9075 (mt) cc_final: 0.8829 (pt) REVERT: Q 27 ILE cc_start: 0.8924 (mt) cc_final: 0.8146 (mt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1785 time to fit residues: 50.4822 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 81 optimal weight: 0.1980 chunk 158 optimal weight: 50.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035793 restraints weight = 106240.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035837 restraints weight = 98123.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.035871 restraints weight = 94805.433| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10532 Z= 0.122 Angle : 0.482 8.069 14490 Z= 0.278 Chirality : 0.040 0.191 1931 Planarity : 0.005 0.078 1962 Dihedral : 3.768 14.411 1819 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 2.48 (0.20), residues: 1771 helix: 2.33 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.40 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.026 0.001 PHE J 55 TYR 0.010 0.001 TYR J 48 ARG 0.003 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1143) hydrogen bonds : angle 3.57151 ( 3417) covalent geometry : bond 0.00243 (10532) covalent geometry : angle 0.48221 (14490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.8603 (mt) cc_final: 0.8366 (mt) REVERT: K 41 ILE cc_start: 0.8357 (tp) cc_final: 0.8011 (tp) REVERT: K 43 ASN cc_start: 0.8751 (p0) cc_final: 0.8379 (m-40) REVERT: L 49 MET cc_start: 0.8105 (ptt) cc_final: 0.7767 (ptt) REVERT: M 32 VAL cc_start: 0.8467 (t) cc_final: 0.7299 (t) REVERT: O 27 ILE cc_start: 0.9729 (mt) cc_final: 0.9419 (mt) REVERT: P 27 ILE cc_start: 0.9395 (mm) cc_final: 0.9103 (mm) REVERT: P 32 VAL cc_start: 0.9621 (p) cc_final: 0.9404 (p) REVERT: P 70 ILE cc_start: 0.4019 (mm) cc_final: 0.3776 (mt) REVERT: Q 24 ILE cc_start: 0.8589 (mt) cc_final: 0.8001 (pt) REVERT: Q 27 ILE cc_start: 0.8077 (mt) cc_final: 0.6424 (mt) REVERT: Q 57 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8074 (mm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1879 time to fit residues: 54.2042 Evaluate side-chains 134 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 1 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 81 optimal weight: 0.0050 chunk 5 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 166 optimal weight: 40.0000 chunk 141 optimal weight: 40.0000 chunk 123 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.036464 restraints weight = 109456.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036508 restraints weight = 101711.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036508 restraints weight = 98479.062| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10532 Z= 0.134 Angle : 0.488 6.066 14490 Z= 0.285 Chirality : 0.041 0.207 1931 Planarity : 0.005 0.077 1962 Dihedral : 3.748 15.310 1819 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 2.55 (0.20), residues: 1771 helix: 2.33 (0.13), residues: 1449 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.035 0.001 PHE K 62 TYR 0.007 0.001 TYR J 48 ARG 0.007 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1143) hydrogen bonds : angle 3.56663 ( 3417) covalent geometry : bond 0.00277 (10532) covalent geometry : angle 0.48815 (14490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.8853 (mt) cc_final: 0.8616 (mt) REVERT: J 68 PHE cc_start: 0.8720 (m-10) cc_final: 0.8468 (m-80) REVERT: K 27 ILE cc_start: 0.9487 (mt) cc_final: 0.9285 (mt) REVERT: K 41 ILE cc_start: 0.8746 (tp) cc_final: 0.8407 (tp) REVERT: K 43 ASN cc_start: 0.9213 (p0) cc_final: 0.9005 (m-40) REVERT: M 27 ILE cc_start: 0.9500 (mt) cc_final: 0.9262 (mt) REVERT: P 27 ILE cc_start: 0.9578 (mm) cc_final: 0.9376 (mm) REVERT: P 61 ILE cc_start: 0.8019 (mm) cc_final: 0.7784 (pt) REVERT: P 70 ILE cc_start: 0.6120 (mm) cc_final: 0.5831 (mt) REVERT: Q 24 ILE cc_start: 0.9019 (mt) cc_final: 0.8511 (pt) REVERT: Q 27 ILE cc_start: 0.9190 (mt) cc_final: 0.8181 (mt) REVERT: Q 57 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8360 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1627 time to fit residues: 43.4129 Evaluate side-chains 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.036372 restraints weight = 111452.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036459 restraints weight = 102488.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036461 restraints weight = 98674.614| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10532 Z= 0.212 Angle : 0.548 6.279 14490 Z= 0.326 Chirality : 0.042 0.201 1931 Planarity : 0.005 0.081 1962 Dihedral : 4.038 16.445 1819 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 2.25 (0.20), residues: 1771 helix: 2.11 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.37 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.015 0.002 PHE K 50 TYR 0.007 0.001 TYR M 48 ARG 0.007 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1143) hydrogen bonds : angle 3.87296 ( 3417) covalent geometry : bond 0.00378 (10532) covalent geometry : angle 0.54820 (14490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.8025 (tpt) cc_final: 0.7208 (tpt) REVERT: J 68 PHE cc_start: 0.8902 (m-10) cc_final: 0.8643 (m-80) REVERT: K 5 ASN cc_start: 0.9837 (p0) cc_final: 0.9576 (m-40) REVERT: K 41 ILE cc_start: 0.8973 (tp) cc_final: 0.8573 (tp) REVERT: K 43 ASN cc_start: 0.9250 (p0) cc_final: 0.9003 (m-40) REVERT: L 24 ILE cc_start: 0.9764 (mp) cc_final: 0.9551 (pt) REVERT: P 70 ILE cc_start: 0.6711 (mm) cc_final: 0.6389 (mt) REVERT: Q 24 ILE cc_start: 0.9276 (mt) cc_final: 0.8923 (pt) REVERT: Q 27 ILE cc_start: 0.9489 (mt) cc_final: 0.8938 (mt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1555 time to fit residues: 40.2587 Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 118 optimal weight: 0.0570 chunk 145 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 112 optimal weight: 0.2980 chunk 130 optimal weight: 30.0000 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.036318 restraints weight = 108960.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036441 restraints weight = 100063.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036552 restraints weight = 96472.308| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10532 Z= 0.126 Angle : 0.489 6.289 14490 Z= 0.283 Chirality : 0.041 0.194 1931 Planarity : 0.005 0.079 1962 Dihedral : 3.781 16.270 1819 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 2.59 (0.20), residues: 1771 helix: 2.32 (0.13), residues: 1451 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.034 0.001 PHE H 50 TYR 0.008 0.001 TYR H 48 ARG 0.006 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1143) hydrogen bonds : angle 3.58335 ( 3417) covalent geometry : bond 0.00254 (10532) covalent geometry : angle 0.48921 (14490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.8146 (tpt) cc_final: 0.7433 (tpt) REVERT: J 68 PHE cc_start: 0.8699 (m-10) cc_final: 0.8463 (m-80) REVERT: K 41 ILE cc_start: 0.8813 (tp) cc_final: 0.8435 (tp) REVERT: K 43 ASN cc_start: 0.9137 (p0) cc_final: 0.8869 (m-40) REVERT: P 70 ILE cc_start: 0.5841 (mm) cc_final: 0.5491 (mt) REVERT: Q 24 ILE cc_start: 0.8970 (mt) cc_final: 0.8482 (pt) REVERT: Q 27 ILE cc_start: 0.9307 (mt) cc_final: 0.8252 (mt) REVERT: Q 57 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8358 (mm-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1639 time to fit residues: 41.6829 Evaluate side-chains 126 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036071 restraints weight = 108198.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036214 restraints weight = 98458.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036313 restraints weight = 94398.498| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10532 Z= 0.200 Angle : 0.550 7.540 14490 Z= 0.327 Chirality : 0.042 0.197 1931 Planarity : 0.005 0.075 1962 Dihedral : 4.029 17.270 1819 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 2.37 (0.20), residues: 1771 helix: 2.24 (0.13), residues: 1431 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.044 0.002 PHE K 62 TYR 0.006 0.001 TYR M 48 ARG 0.006 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1143) hydrogen bonds : angle 3.82955 ( 3417) covalent geometry : bond 0.00361 (10532) covalent geometry : angle 0.55002 (14490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 PHE cc_start: 0.8776 (m-10) cc_final: 0.8536 (m-80) REVERT: K 5 ASN cc_start: 0.9817 (p0) cc_final: 0.9548 (m-40) REVERT: K 41 ILE cc_start: 0.8763 (tp) cc_final: 0.8363 (tp) REVERT: K 43 ASN cc_start: 0.9128 (p0) cc_final: 0.8856 (m-40) REVERT: P 70 ILE cc_start: 0.6127 (mm) cc_final: 0.5749 (mt) REVERT: Q 27 ILE cc_start: 0.9404 (mt) cc_final: 0.8916 (mt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1654 time to fit residues: 41.5766 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 108 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 155 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 50.0000 chunk 92 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.037032 restraints weight = 121884.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.037118 restraints weight = 111374.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.037118 restraints weight = 106953.731| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10532 Z= 0.274 Angle : 0.633 7.600 14490 Z= 0.382 Chirality : 0.044 0.208 1931 Planarity : 0.005 0.078 1962 Dihedral : 4.542 18.125 1819 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.46 (0.20), residues: 1771 helix: 1.59 (0.13), residues: 1430 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP Z 122 PHE 0.034 0.003 PHE K 62 TYR 0.007 0.001 TYR K 48 ARG 0.006 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 1143) hydrogen bonds : angle 4.32415 ( 3417) covalent geometry : bond 0.00475 (10532) covalent geometry : angle 0.63335 (14490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4080.75 seconds wall clock time: 73 minutes 16.46 seconds (4396.46 seconds total)