Starting phenix.real_space_refine on Wed Sep 17 18:25:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ity_60883/09_2025/9ity_60883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ity_60883/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ity_60883/09_2025/9ity_60883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ity_60883/09_2025/9ity_60883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ity_60883/09_2025/9ity_60883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ity_60883/09_2025/9ity_60883.map" } resolution = 4.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} 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: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} 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: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} 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: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} 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: {'ARG:plan': 7, 'PHE:plan': 34, 'TYR:plan': 7, 'HIS:plan': 2, 'GLU:plan': 9, 'ASP:plan': 4, 'ASN:plan1': 12, 'GLN:plan1': 4, 'TRP:plan': 2} 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: {'ASN:plan1': 12, 'PHE:plan': 30, 'ASP:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 7, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 2.81, per 1000 atoms: 0.27 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: 1.29 Conformation dependent library (CDL) restraints added in 528.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.22 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: 1.77 Time building geometry restraints manager: 1.61 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: 6.370 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG N 44 TYR 0.005 0.001 TYR H 48 PHE 0.008 0.001 PHE P 62 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00228 (10532) covalent geometry : angle 0.48006 (14490) hydrogen bonds : bond 0.24063 ( 1143) hydrogen bonds : angle 6.06046 ( 3417) *********************** 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 : 0.413 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: 0.0736 time to fit residues: 26.1016 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3063 r_free = 0.3063 target = 0.053024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036140 restraints weight = 114304.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036333 restraints weight = 102152.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.036350 restraints weight = 96186.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036424 restraints weight = 95457.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036452 restraints weight = 93100.867| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4885 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10532 Z= 0.230 Angle : 0.569 8.098 14490 Z= 0.340 Chirality : 0.041 0.193 1931 Planarity : 0.005 0.071 1962 Dihedral : 4.290 18.033 1819 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.20), residues: 1771 helix: 1.81 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 37 TYR 0.012 0.001 TYR K 48 PHE 0.032 0.002 PHE H 62 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00383 (10532) covalent geometry : angle 0.56856 (14490) hydrogen bonds : bond 0.05800 ( 1143) hydrogen bonds : angle 4.44346 ( 3417) *********************** 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 183 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.396 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: 0.9078 (mt) cc_final: 0.8607 (mt) REVERT: J 27 ILE cc_start: 0.9784 (tp) cc_final: 0.9470 (pt) REVERT: K 24 ILE cc_start: 0.8706 (mt) cc_final: 0.8371 (mm) REVERT: K 41 ILE cc_start: 0.8682 (tp) cc_final: 0.8373 (tp) REVERT: K 43 ASN cc_start: 0.9018 (p0) cc_final: 0.8780 (m-40) REVERT: L 49 MET cc_start: 0.8601 (tmm) cc_final: 0.8056 (mmt) REVERT: P 70 ILE cc_start: 0.4937 (mm) cc_final: 0.4632 (mt) REVERT: Q 24 ILE cc_start: 0.8810 (mt) cc_final: 0.8493 (pt) REVERT: Q 32 VAL cc_start: 0.9160 (p) cc_final: 0.8951 (p) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.0719 time to fit residues: 20.8878 Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 169 optimal weight: 50.0000 chunk 122 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 50.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.053471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036229 restraints weight = 112589.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036308 restraints weight = 104055.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.036406 restraints weight = 97728.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036415 restraints weight = 94165.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036415 restraints weight = 93943.209| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10532 Z= 0.189 Angle : 0.537 7.282 14490 Z= 0.313 Chirality : 0.040 0.204 1931 Planarity : 0.005 0.074 1962 Dihedral : 4.129 17.173 1819 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.20), residues: 1771 helix: 1.82 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 37 TYR 0.009 0.001 TYR K 48 PHE 0.020 0.002 PHE Q 50 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00334 (10532) covalent geometry : angle 0.53654 (14490) hydrogen bonds : bond 0.04923 ( 1143) hydrogen bonds : angle 4.13923 ( 3417) *********************** 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 185 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.398 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: symmetry clash REVERT: H 27 ILE cc_start: 0.9376 (mt) cc_final: 0.8917 (mt) REVERT: H 28 VAL cc_start: 0.9378 (t) cc_final: 0.9131 (t) REVERT: H 56 THR cc_start: 0.2258 (p) cc_final: 0.1781 (p) REVERT: K 24 ILE cc_start: 0.9079 (mt) cc_final: 0.8818 (pt) REVERT: K 41 ILE cc_start: 0.8953 (tp) cc_final: 0.8671 (tp) REVERT: K 43 ASN cc_start: 0.9153 (p0) cc_final: 0.8936 (m-40) REVERT: L 4 LEU cc_start: 0.9484 (mt) cc_final: 0.9182 (mt) REVERT: M 27 ILE cc_start: 0.9391 (mt) cc_final: 0.9125 (mt) REVERT: P 27 ILE cc_start: 0.9644 (mm) cc_final: 0.9417 (mm) REVERT: P 70 ILE cc_start: 0.5881 (mm) cc_final: 0.5644 (mt) REVERT: Q 24 ILE cc_start: 0.9093 (mt) cc_final: 0.8809 (mt) REVERT: Q 53 ILE cc_start: 0.5502 (mt) cc_final: 0.4935 (mt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0824 time to fit residues: 23.3326 Evaluate side-chains 137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 59 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 48 optimal weight: 80.0000 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 50.0000 chunk 88 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036397 restraints weight = 112330.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036474 restraints weight = 105293.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036484 restraints weight = 99238.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036484 restraints weight = 98743.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036484 restraints weight = 98743.215| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5021 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10532 Z= 0.147 Angle : 0.489 6.510 14490 Z= 0.286 Chirality : 0.040 0.177 1931 Planarity : 0.005 0.078 1962 Dihedral : 3.967 15.340 1819 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.20), residues: 1771 helix: 1.98 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.51 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 37 TYR 0.007 0.001 TYR J 48 PHE 0.020 0.001 PHE J 55 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00277 (10532) covalent geometry : angle 0.48873 (14490) hydrogen bonds : bond 0.04347 ( 1143) hydrogen bonds : angle 3.85150 ( 3417) *********************** 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 182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.395 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: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9025 (mt) cc_final: 0.8581 (mt) REVERT: I 27 ILE cc_start: 0.8887 (pt) cc_final: 0.8586 (pt) REVERT: K 41 ILE cc_start: 0.8696 (tp) cc_final: 0.8335 (tp) REVERT: K 43 ASN cc_start: 0.8997 (p0) cc_final: 0.8673 (m-40) REVERT: O 27 ILE cc_start: 0.9696 (mt) cc_final: 0.9298 (mt) REVERT: P 27 ILE cc_start: 0.9553 (mm) cc_final: 0.9223 (mm) REVERT: P 53 ILE cc_start: 0.4880 (mt) cc_final: 0.4647 (mt) REVERT: P 70 ILE cc_start: 0.4674 (mm) cc_final: 0.4456 (mt) REVERT: Q 24 ILE cc_start: 0.8777 (mt) cc_final: 0.8414 (mt) REVERT: Q 27 ILE cc_start: 0.7990 (mt) cc_final: 0.6993 (mt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0707 time to fit residues: 20.1875 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 30 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 47 optimal weight: 60.0000 chunk 39 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036312 restraints weight = 111862.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.036379 restraints weight = 103004.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036494 restraints weight = 98323.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036497 restraints weight = 95029.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036497 restraints weight = 94948.879| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4974 moved from start: 0.3647 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= 0.158 Angle : 0.504 6.726 14490 Z= 0.294 Chirality : 0.040 0.176 1931 Planarity : 0.005 0.077 1962 Dihedral : 3.953 16.010 1819 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.20), residues: 1771 helix: 2.14 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -1.57 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 37 TYR 0.006 0.001 TYR K 48 PHE 0.018 0.001 PHE Q 55 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00291 (10532) covalent geometry : angle 0.50361 (14490) hydrogen bonds : bond 0.04278 ( 1143) hydrogen bonds : angle 3.77670 ( 3417) *********************** 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 176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.384 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: 0.8833 (mt) cc_final: 0.8555 (mt) REVERT: H 28 VAL cc_start: 0.9239 (t) cc_final: 0.9032 (t) REVERT: H 35 ILE cc_start: 0.5534 (mm) cc_final: 0.4830 (mm) REVERT: K 41 ILE cc_start: 0.8587 (tp) cc_final: 0.8250 (tp) REVERT: K 43 ASN cc_start: 0.8959 (p0) cc_final: 0.8659 (m-40) REVERT: K 56 THR cc_start: 0.2694 (p) cc_final: 0.2232 (t) REVERT: L 24 ILE cc_start: 0.9422 (mp) cc_final: 0.9167 (pt) REVERT: O 27 ILE cc_start: 0.9740 (mt) cc_final: 0.9540 (mt) REVERT: P 27 ILE cc_start: 0.9608 (mm) cc_final: 0.9334 (mm) REVERT: P 70 ILE cc_start: 0.4365 (mm) cc_final: 0.4121 (mt) REVERT: Q 24 ILE cc_start: 0.8828 (mt) cc_final: 0.8432 (pt) REVERT: Q 27 ILE cc_start: 0.8291 (mt) cc_final: 0.7386 (mt) REVERT: Q 32 VAL cc_start: 0.9228 (p) cc_final: 0.8989 (p) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0656 time to fit residues: 18.2651 Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.036049 restraints weight = 110448.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036136 restraints weight = 100359.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036154 restraints weight = 96589.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036154 restraints weight = 95955.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036154 restraints weight = 95955.649| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10532 Z= 0.125 Angle : 0.480 6.788 14490 Z= 0.276 Chirality : 0.039 0.171 1931 Planarity : 0.005 0.077 1962 Dihedral : 3.730 14.166 1819 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.20), residues: 1771 helix: 2.36 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -1.44 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 37 TYR 0.007 0.001 TYR H 48 PHE 0.040 0.002 PHE J 68 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00244 (10532) covalent geometry : angle 0.48012 (14490) hydrogen bonds : bond 0.03845 ( 1143) hydrogen bonds : angle 3.54640 ( 3417) *********************** 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 179 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.395 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: 0.8732 (mt) cc_final: 0.8421 (mt) REVERT: K 41 ILE cc_start: 0.8430 (tp) cc_final: 0.8110 (tp) REVERT: K 43 ASN cc_start: 0.8879 (p0) cc_final: 0.8550 (m-40) REVERT: M 27 ILE cc_start: 0.8874 (mt) cc_final: 0.8647 (mt) REVERT: M 32 VAL cc_start: 0.7690 (t) cc_final: 0.7190 (t) REVERT: O 27 ILE cc_start: 0.9783 (mt) cc_final: 0.9503 (mt) REVERT: P 27 ILE cc_start: 0.9429 (mm) cc_final: 0.9072 (mm) REVERT: P 70 ILE cc_start: 0.4048 (mm) cc_final: 0.3796 (mt) REVERT: Q 24 ILE cc_start: 0.8688 (mt) cc_final: 0.8322 (pt) REVERT: Q 27 ILE cc_start: 0.8154 (mt) cc_final: 0.7439 (mt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0773 time to fit residues: 21.7389 Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 129 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 11 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 overall best weight: 3.7324 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.053623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.036405 restraints weight = 109746.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036435 restraints weight = 104309.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036435 restraints weight = 99213.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036435 restraints weight = 99213.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.036435 restraints weight = 99213.082| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10532 Z= 0.208 Angle : 0.545 7.219 14490 Z= 0.324 Chirality : 0.042 0.214 1931 Planarity : 0.005 0.076 1962 Dihedral : 3.967 15.260 1819 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.20), residues: 1771 helix: 2.11 (0.13), residues: 1438 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 37 TYR 0.007 0.001 TYR M 48 PHE 0.032 0.002 PHE J 68 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00381 (10532) covalent geometry : angle 0.54516 (14490) hydrogen bonds : bond 0.04435 ( 1143) hydrogen bonds : angle 3.84978 ( 3417) *********************** 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 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.7511 (tmm) cc_final: 0.6142 (tmm) REVERT: K 41 ILE cc_start: 0.9045 (tp) cc_final: 0.8671 (tp) REVERT: P 70 ILE cc_start: 0.6671 (mm) cc_final: 0.6348 (mt) REVERT: Q 24 ILE cc_start: 0.9305 (mt) cc_final: 0.9054 (mt) REVERT: Q 27 ILE cc_start: 0.9351 (mt) cc_final: 0.8813 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0783 time to fit residues: 20.1309 Evaluate side-chains 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 160 optimal weight: 0.2980 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 161 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.036166 restraints weight = 111887.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036247 restraints weight = 102557.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036247 restraints weight = 99987.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036247 restraints weight = 99986.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036247 restraints weight = 99986.884| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.4335 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= 0.167 Angle : 0.521 8.577 14490 Z= 0.303 Chirality : 0.041 0.212 1931 Planarity : 0.005 0.079 1962 Dihedral : 3.921 15.686 1819 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.20), residues: 1771 helix: 2.21 (0.13), residues: 1435 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 37 TYR 0.006 0.001 TYR M 48 PHE 0.027 0.002 PHE J 68 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00317 (10532) covalent geometry : angle 0.52108 (14490) hydrogen bonds : bond 0.04150 ( 1143) hydrogen bonds : angle 3.73828 ( 3417) *********************** 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 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.6687 (tmm) cc_final: 0.6469 (tmm) REVERT: M 27 ILE cc_start: 0.9310 (mt) cc_final: 0.9098 (mt) REVERT: P 27 ILE cc_start: 0.9701 (mm) cc_final: 0.9489 (mm) REVERT: P 53 ILE cc_start: 0.5228 (mt) cc_final: 0.4903 (mt) REVERT: P 70 ILE cc_start: 0.5909 (mm) cc_final: 0.5548 (mt) REVERT: Q 24 ILE cc_start: 0.9124 (mt) cc_final: 0.8796 (pt) REVERT: Q 27 ILE cc_start: 0.9241 (mt) cc_final: 0.8396 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0771 time to fit residues: 19.1329 Evaluate side-chains 120 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 5 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.053920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.036389 restraints weight = 110469.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036465 restraints weight = 100410.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036465 restraints weight = 96634.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036465 restraints weight = 96632.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036465 restraints weight = 96632.394| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10532 Z= 0.202 Angle : 0.550 8.672 14490 Z= 0.327 Chirality : 0.042 0.220 1931 Planarity : 0.005 0.077 1962 Dihedral : 4.118 16.981 1819 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.20), residues: 1771 helix: 2.00 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.57 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 37 TYR 0.008 0.001 TYR H 48 PHE 0.035 0.002 PHE K 62 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00365 (10532) covalent geometry : angle 0.55038 (14490) hydrogen bonds : bond 0.04421 ( 1143) hydrogen bonds : angle 3.92341 ( 3417) *********************** 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 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.6710 (tmm) cc_final: 0.6424 (tmm) REVERT: K 5 ASN cc_start: 0.9813 (p0) cc_final: 0.9537 (m-40) REVERT: O 55 PHE cc_start: 0.9354 (m-80) cc_final: 0.9142 (m-80) REVERT: P 70 ILE cc_start: 0.6254 (mm) cc_final: 0.5874 (mt) REVERT: Q 24 ILE cc_start: 0.9272 (mt) cc_final: 0.8978 (pt) REVERT: Q 27 ILE cc_start: 0.9413 (mt) cc_final: 0.8784 (mt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0776 time to fit residues: 18.9822 Evaluate side-chains 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.053648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036896 restraints weight = 113658.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036962 restraints weight = 106830.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036962 restraints weight = 100344.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036962 restraints weight = 100344.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036962 restraints weight = 100344.291| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10532 Z= 0.234 Angle : 0.584 9.423 14490 Z= 0.348 Chirality : 0.043 0.219 1931 Planarity : 0.005 0.077 1962 Dihedral : 4.318 17.806 1819 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.20), residues: 1771 helix: 1.78 (0.13), residues: 1431 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 37 TYR 0.008 0.001 TYR K 48 PHE 0.035 0.002 PHE K 62 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00410 (10532) covalent geometry : angle 0.58387 (14490) hydrogen bonds : bond 0.04648 ( 1143) hydrogen bonds : angle 4.09370 ( 3417) ********************** 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 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 ASN cc_start: 0.9835 (p0) cc_final: 0.9559 (m-40) REVERT: O 55 PHE cc_start: 0.9241 (m-80) cc_final: 0.8944 (m-80) REVERT: P 70 ILE cc_start: 0.6504 (mm) cc_final: 0.6124 (mt) REVERT: Q 24 ILE cc_start: 0.9359 (mt) cc_final: 0.9044 (pt) REVERT: Q 27 ILE cc_start: 0.9488 (mt) cc_final: 0.8893 (mt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0787 time to fit residues: 19.0563 Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 157 optimal weight: 50.0000 chunk 173 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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** ** L 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 = 0.3071 r_free = 0.3071 target = 0.053493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036369 restraints weight = 112226.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036419 restraints weight = 105204.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036419 restraints weight = 101303.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036419 restraints weight = 101303.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.036419 restraints weight = 101303.919| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10532 Z= 0.202 Angle : 0.555 8.486 14490 Z= 0.329 Chirality : 0.042 0.213 1931 Planarity : 0.005 0.077 1962 Dihedral : 4.244 17.657 1819 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.20), residues: 1771 helix: 1.86 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 37 TYR 0.006 0.001 TYR J 48 PHE 0.032 0.002 PHE K 62 TRP 0.000 0.000 TRP Z 122 Details of bonding type rmsd covalent geometry : bond 0.00362 (10532) covalent geometry : angle 0.55539 (14490) hydrogen bonds : bond 0.04458 ( 1143) hydrogen bonds : angle 3.97288 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.57 seconds wall clock time: 34 minutes 28.67 seconds (2068.67 seconds total)