Starting phenix.real_space_refine on Thu Feb 5 08:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uv4_64523/02_2026/9uv4_64523.map" } resolution = 3.3 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= 0.013 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 54 5.16 5 C 9979 2.51 5 N 2766 2.21 5 O 3015 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15814 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 836 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "M" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 718 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 836 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "N" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 718 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 836 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "O" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 718 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3721 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 18, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 632 Unresolved non-hydrogen angles: 818 Unresolved non-hydrogen dihedrals: 487 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 16, 'ASP:plan': 16, 'GLN:plan1': 9, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 337 Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3714 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 18, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 827 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 16, 'ASP:plan': 17, 'GLN:plan1': 9, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 340 Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3717 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 18, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 635 Unresolved non-hydrogen angles: 822 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 16, 'ASP:plan': 17, 'GLN:plan1': 9, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 3.66, per 1000 atoms: 0.23 Number of scatterers: 15814 At special positions: 0 Unit cell: (166.52, 151.8, 179.4, 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 54 16.00 O 3015 8.00 N 2766 7.00 C 9979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 87 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 482 " distance=1.90 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 482 " distance=1.90 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 364 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 508.3 milliseconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4314 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 46 sheets defined 11.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'I' and resid 53 through 56 removed outlier: 3.817A pdb=" N SER I 56 " --> pdb=" O PRO I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'M' and resid 78 through 82 removed outlier: 3.525A pdb=" N ASP M 81 " --> pdb=" O GLU M 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA M 82 " --> pdb=" O ALA M 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 78 through 82' Processing helix chain 'J' and resid 53 through 56 removed outlier: 3.817A pdb=" N SER J 56 " --> pdb=" O PRO J 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 53 through 56' Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.525A pdb=" N ASP N 81 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA N 82 " --> pdb=" O ALA N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 82' Processing helix chain 'K' and resid 53 through 56 removed outlier: 3.817A pdb=" N SER K 56 " --> pdb=" O PRO K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 56' Processing helix chain 'O' and resid 78 through 82 removed outlier: 3.525A pdb=" N ASP O 81 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA O 82 " --> pdb=" O ALA O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 82' Processing helix chain 'A' and resid 146 through 153 removed outlier: 3.598A pdb=" N GLY A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 380 Processing helix chain 'A' and resid 451 through 496 removed outlier: 3.782A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.595A pdb=" N VAL A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 removed outlier: 3.597A pdb=" N GLY B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 152 " --> pdb=" O TRP B 148 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 380 Processing helix chain 'B' and resid 451 through 496 removed outlier: 3.782A pdb=" N ALA B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.596A pdb=" N VAL B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.598A pdb=" N GLY C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 380 Processing helix chain 'C' and resid 451 through 496 removed outlier: 3.781A pdb=" N ALA C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.596A pdb=" N VAL C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS I 22 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL I 18 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS I 22 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR I 80 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU I 82 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR I 69 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.722A pdb=" N ASN I 59 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE I 34 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR I 95 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 39 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL I 93 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 98 " --> pdb=" O TYR I 107 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR I 107 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.722A pdb=" N ASN I 59 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE I 34 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR I 95 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN I 39 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL I 93 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.730A pdb=" N SER M 24 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET M 21 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS M 23 " --> pdb=" O TYR M 70 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR M 70 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER M 71 " --> pdb=" O SER M 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.538A pdb=" N GLU M 104 " --> pdb=" O MET M 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 44 through 47 removed outlier: 5.997A pdb=" N LEU M 45 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN M 36 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE M 47 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP M 34 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS J 22 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS J 22 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR J 80 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 82 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR J 69 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.722A pdb=" N ASN J 59 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN J 50 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE J 34 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP J 33 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR J 95 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 39 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG J 98 " --> pdb=" O TYR J 107 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.722A pdb=" N ASN J 59 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN J 50 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE J 34 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP J 33 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR J 95 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 39 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.731A pdb=" N SER N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET N 21 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS N 23 " --> pdb=" O TYR N 70 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR N 70 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER N 71 " --> pdb=" O SER N 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 13 removed outlier: 3.538A pdb=" N GLU N 104 " --> pdb=" O MET N 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 44 through 47 removed outlier: 5.997A pdb=" N LEU N 45 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN N 36 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE N 47 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP N 34 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS K 22 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.597A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS K 22 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP K 73 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR K 80 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR K 71 " --> pdb=" O TYR K 80 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU K 82 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR K 69 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.723A pdb=" N ASN K 59 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN K 50 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE K 34 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR K 97 " --> pdb=" O ASN K 35 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL K 37 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR K 95 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 39 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL K 93 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG K 98 " --> pdb=" O TYR K 107 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.723A pdb=" N ASN K 59 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN K 50 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE K 34 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR K 97 " --> pdb=" O ASN K 35 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL K 37 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR K 95 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN K 39 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL K 93 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.731A pdb=" N SER O 24 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET O 21 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS O 23 " --> pdb=" O TYR O 70 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR O 70 " --> pdb=" O CYS O 23 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER O 71 " --> pdb=" O SER O 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 11 through 13 removed outlier: 3.538A pdb=" N GLU O 104 " --> pdb=" O MET O 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 44 through 47 removed outlier: 5.997A pdb=" N LEU O 45 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN O 36 " --> pdb=" O LEU O 45 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE O 47 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP O 34 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 67 through 68 removed outlier: 4.156A pdb=" N PHE A 67 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.716A pdb=" N THR A 78 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 620 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG A 80 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS A 338 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 324 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 102 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A 100 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 96 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 97 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 99 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS A 338 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 324 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 102 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A 100 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 96 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 97 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 99 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.565A pdb=" N ILE A 226 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS A 113 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A 308 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.891A pdb=" N LYS A 119 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AD2, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AD3, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.086A pdb=" N THR A 255 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AD5, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS B 338 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU B 100 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 96 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 97 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 99 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS B 338 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU B 100 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 96 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 97 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 99 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.565A pdb=" N ILE B 226 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS B 113 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS B 308 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 140 through 143 removed outlier: 3.891A pdb=" N LYS B 119 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AE1, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AE2, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.086A pdb=" N THR B 255 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 618 through 619 removed outlier: 7.235A pdb=" N ALA B 618 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 77 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 522 " --> pdb=" O GLU C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS C 338 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU C 100 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 96 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 97 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 99 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.530A pdb=" N HIS C 338 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU C 100 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 96 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 97 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 99 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 187 through 188 removed outlier: 3.565A pdb=" N ILE C 226 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS C 113 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS C 308 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.891A pdb=" N LYS C 119 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AE9, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AF1, first strand: chain 'C' and resid 255 through 256 removed outlier: 4.086A pdb=" N THR C 255 " --> pdb=" O SER C 262 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1209 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: 2.22 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5235 1.34 - 1.46: 3918 1.46 - 1.58: 6944 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 16175 Sorted by residual: bond pdb=" N LEU C 100 " pdb=" CA LEU C 100 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.23e-02 6.61e+03 4.48e+00 bond pdb=" CA ALA C 289 " pdb=" CB ALA C 289 " ideal model delta sigma weight residual 1.532 1.506 0.026 1.26e-02 6.30e+03 4.32e+00 bond pdb=" CA ALA A 289 " pdb=" CB ALA A 289 " ideal model delta sigma weight residual 1.532 1.506 0.026 1.26e-02 6.30e+03 4.31e+00 bond pdb=" CA ALA B 289 " pdb=" CB ALA B 289 " ideal model delta sigma weight residual 1.532 1.506 0.026 1.26e-02 6.30e+03 4.27e+00 bond pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta sigma weight residual 1.461 1.438 0.023 1.19e-02 7.06e+03 3.81e+00 ... (remaining 16170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 21720 1.86 - 3.71: 342 3.71 - 5.57: 51 5.57 - 7.43: 3 7.43 - 9.28: 6 Bond angle restraints: 22122 Sorted by residual: angle pdb=" N GLY B 518 " pdb=" CA GLY B 518 " pdb=" C GLY B 518 " ideal model delta sigma weight residual 115.42 107.58 7.84 1.27e+00 6.20e-01 3.81e+01 angle pdb=" N ILE C 107 " pdb=" CA ILE C 107 " pdb=" C ILE C 107 " ideal model delta sigma weight residual 113.43 108.43 5.00 1.09e+00 8.42e-01 2.10e+01 angle pdb=" N VAL A 523 " pdb=" CA VAL A 523 " pdb=" C VAL A 523 " ideal model delta sigma weight residual 110.09 116.95 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" N ILE B 107 " pdb=" CA ILE B 107 " pdb=" C ILE B 107 " ideal model delta sigma weight residual 113.43 108.56 4.87 1.09e+00 8.42e-01 2.00e+01 angle pdb=" N TYR A 103 " pdb=" CA TYR A 103 " pdb=" C TYR A 103 " ideal model delta sigma weight residual 114.39 108.06 6.33 1.45e+00 4.76e-01 1.90e+01 ... (remaining 22117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8433 17.94 - 35.89: 776 35.89 - 53.83: 177 53.83 - 71.78: 37 71.78 - 89.72: 6 Dihedral angle restraints: 9429 sinusoidal: 2721 harmonic: 6708 Sorted by residual: dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 482 " pdb=" CB CYS C 482 " ideal model delta sinusoidal sigma weight residual 93.00 39.37 53.63 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS A 87 " pdb=" SG CYS A 87 " pdb=" SG CYS A 482 " pdb=" CB CYS A 482 " ideal model delta sinusoidal sigma weight residual 93.00 39.46 53.54 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA LYS C 648 " pdb=" C LYS C 648 " pdb=" N LEU C 649 " pdb=" CA LEU C 649 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 9426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2045 0.049 - 0.099: 317 0.099 - 0.148: 119 0.148 - 0.197: 2 0.197 - 0.247: 2 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA TYR C 103 " pdb=" N TYR C 103 " pdb=" C TYR C 103 " pdb=" CB TYR C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LYS B 448 " pdb=" N LYS B 448 " pdb=" C LYS B 448 " pdb=" CB LYS B 448 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TYR A 103 " pdb=" N TYR A 103 " pdb=" C TYR A 103 " pdb=" CB TYR A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2482 not shown) Planarity restraints: 2897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 648 " 0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C LYS C 648 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS C 648 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU C 649 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 648 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS A 648 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS A 648 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 649 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 648 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LYS B 648 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS B 648 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU B 649 " -0.023 2.00e-02 2.50e+03 ... (remaining 2894 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 41 2.41 - 3.03: 9170 3.03 - 3.66: 21286 3.66 - 4.28: 27997 4.28 - 4.90: 47553 Nonbonded interactions: 106047 Sorted by model distance: nonbonded pdb=" CZ3 TRP B 481 " pdb=" CZ3 TRP C 481 " model vdw 1.791 3.640 nonbonded pdb=" CZ3 TRP A 481 " pdb=" CZ3 TRP B 481 " model vdw 1.899 3.640 nonbonded pdb=" CZ3 TRP A 481 " pdb=" CZ3 TRP C 481 " model vdw 1.924 3.640 nonbonded pdb=" CH2 TRP B 481 " pdb=" CE3 TRP C 481 " model vdw 1.955 3.640 nonbonded pdb=" CH2 TRP A 481 " pdb=" CE3 TRP B 481 " model vdw 1.984 3.640 ... (remaining 106042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 62 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 104 or (resid 105 \ through 106 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 7 through 446 or (resid 447 and (name N or name CA or name C or name O or name C \ B )) or resid 448 through 504 or (resid 505 through 507 and (name N or name CA o \ r name C or name O or name CB )) or resid 508 through 652)) selection = (chain 'B' and (resid 62 through 104 or (resid 105 through 106 and (name N or na \ me CA or name C or name O or name CB )) or resid 107 through 652)) selection = (chain 'C' and (resid 62 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O or name CB )) or resid 103 through 446 or (resid 447 and (name N o \ r name CA or name C or name O or name CB )) or resid 448 through 504 or (resid 5 \ 05 through 507 and (name N or name CA or name C or name O or name CB )) or resid \ 508 through 510 or (resid 511 through 515 and (name N or name CA or name C or n \ ame O or name CB )) or resid 516 through 652)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.340 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 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 : 0.003 0.133 16189 Z= 0.183 Angle : 0.591 25.102 22150 Z= 0.338 Chirality : 0.041 0.247 2485 Planarity : 0.003 0.045 2897 Dihedral : 15.255 89.719 5073 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.67 % Rotamer: Outliers : 0.32 % Allowed : 23.98 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 2244 helix: 3.45 (0.36), residues: 231 sheet: 0.49 (0.30), residues: 396 loop : -1.92 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 80 TYR 0.012 0.000 TYR C 103 PHE 0.003 0.000 PHE B 112 TRP 0.004 0.000 TRP N 90 HIS 0.001 0.000 HIS C 592 Details of bonding type rmsd covalent geometry : bond 0.00242 (16175) covalent geometry : angle 0.53880 (22122) SS BOND : bond 0.05019 ( 14) SS BOND : angle 6.84655 ( 28) hydrogen bonds : bond 0.23372 ( 383) hydrogen bonds : angle 8.74597 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.468 Fit side-chains REVERT: A 152 ASP cc_start: 0.7733 (m-30) cc_final: 0.7441 (m-30) REVERT: A 156 ILE cc_start: 0.7817 (tp) cc_final: 0.7527 (pt) REVERT: A 634 ILE cc_start: 0.7560 (mm) cc_final: 0.7344 (pt) outliers start: 4 outliers final: 2 residues processed: 243 average time/residue: 0.1074 time to fit residues: 39.1869 Evaluate side-chains 155 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN O 36 GLN A 335 HIS A 342 ASN A 349 ASN B 404 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 404 GLN ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.079306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057474 restraints weight = 79670.701| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 5.02 r_work: 0.3086 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16189 Z= 0.194 Angle : 0.631 8.300 22150 Z= 0.341 Chirality : 0.044 0.188 2485 Planarity : 0.004 0.047 2897 Dihedral : 4.364 59.817 2466 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.51 % Allowed : 20.80 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2244 helix: 3.10 (0.36), residues: 216 sheet: 0.53 (0.25), residues: 534 loop : -2.13 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 479 TYR 0.023 0.002 TYR C 117 PHE 0.019 0.002 PHE A 153 TRP 0.024 0.002 TRP O 90 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00408 (16175) covalent geometry : angle 0.62596 (22122) SS BOND : bond 0.00372 ( 14) SS BOND : angle 2.33388 ( 28) hydrogen bonds : bond 0.07537 ( 383) hydrogen bonds : angle 4.86974 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: I 40 ARG cc_start: 0.8619 (tpp80) cc_final: 0.7922 (tpt170) REVERT: I 84 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7786 (p) REVERT: M 32 MET cc_start: 0.8580 (mmm) cc_final: 0.8282 (mmm) REVERT: J 3 GLN cc_start: 0.8487 (mp10) cc_final: 0.8168 (tm-30) REVERT: J 40 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8089 (tpt170) REVERT: J 46 GLU cc_start: 0.8979 (tp30) cc_final: 0.8755 (tp30) REVERT: K 40 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7244 (tpt170) REVERT: K 102 ARG cc_start: 0.7927 (mmp80) cc_final: 0.7431 (mmm160) REVERT: A 82 ASP cc_start: 0.9272 (t0) cc_final: 0.9000 (t0) REVERT: A 165 MET cc_start: 0.5973 (mmm) cc_final: 0.5552 (mmm) REVERT: A 342 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8797 (t0) REVERT: B 165 MET cc_start: 0.7670 (mmm) cc_final: 0.7354 (tpp) REVERT: B 601 TYR cc_start: 0.7304 (p90) cc_final: 0.7039 (p90) REVERT: B 631 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8965 (mm) REVERT: C 482 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (t) REVERT: C 559 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7146 (p90) outliers start: 44 outliers final: 17 residues processed: 189 average time/residue: 0.1370 time to fit residues: 38.0149 Evaluate side-chains 158 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 140 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 0.0170 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 overall best weight: 2.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 GLN O 36 GLN A 330 GLN A 404 GLN A 592 HIS B 330 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.074702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.052367 restraints weight = 78448.541| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.86 r_work: 0.2953 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16189 Z= 0.192 Angle : 0.577 8.925 22150 Z= 0.310 Chirality : 0.044 0.198 2485 Planarity : 0.004 0.058 2897 Dihedral : 4.236 58.643 2465 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.27 % Allowed : 22.55 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 2244 helix: 3.52 (0.37), residues: 213 sheet: 0.50 (0.24), residues: 561 loop : -2.21 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 60 TYR 0.027 0.002 TYR A 103 PHE 0.018 0.002 PHE C 256 TRP 0.015 0.001 TRP A 481 HIS 0.007 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00434 (16175) covalent geometry : angle 0.57453 (22122) SS BOND : bond 0.00471 ( 14) SS BOND : angle 1.48817 ( 28) hydrogen bonds : bond 0.06226 ( 383) hydrogen bonds : angle 4.56338 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: I 40 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8167 (tpt170) REVERT: I 102 ARG cc_start: 0.7918 (mmp80) cc_final: 0.7322 (mmm160) REVERT: J 40 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8161 (tpt170) REVERT: J 46 GLU cc_start: 0.9073 (tp30) cc_final: 0.8845 (tp30) REVERT: N 21 MET cc_start: 0.8892 (pmm) cc_final: 0.8549 (pmm) REVERT: N 32 MET cc_start: 0.8795 (mmm) cc_final: 0.8351 (mmm) REVERT: K 3 GLN cc_start: 0.8992 (mp10) cc_final: 0.8517 (mp10) REVERT: K 102 ARG cc_start: 0.8114 (mmp80) cc_final: 0.7608 (mmm160) REVERT: O 11 MET cc_start: 0.7779 (pmm) cc_final: 0.7431 (pmm) REVERT: A 82 ASP cc_start: 0.9441 (t0) cc_final: 0.9059 (t0) REVERT: A 165 MET cc_start: 0.6891 (mmm) cc_final: 0.6669 (tpp) REVERT: A 238 ASN cc_start: 0.7703 (p0) cc_final: 0.7313 (t0) REVERT: A 516 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8753 (m-10) REVERT: A 601 TYR cc_start: 0.7368 (p90) cc_final: 0.6903 (p90) REVERT: B 367 ASP cc_start: 0.9336 (m-30) cc_final: 0.9111 (p0) REVERT: B 482 CYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8937 (t) REVERT: B 601 TYR cc_start: 0.7176 (p90) cc_final: 0.6906 (p90) REVERT: C 559 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (p90) outliers start: 41 outliers final: 18 residues processed: 174 average time/residue: 0.1465 time to fit residues: 36.9077 Evaluate side-chains 153 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 93 TYR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 48 optimal weight: 0.0040 chunk 53 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 HIS C 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.072277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049988 restraints weight = 78488.731| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.74 r_work: 0.2888 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16189 Z= 0.204 Angle : 0.583 9.288 22150 Z= 0.311 Chirality : 0.044 0.199 2485 Planarity : 0.004 0.058 2897 Dihedral : 4.425 59.293 2465 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.98 % Allowed : 22.47 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2244 helix: 3.30 (0.37), residues: 216 sheet: 0.47 (0.23), residues: 609 loop : -2.28 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 44 TYR 0.021 0.002 TYR C 117 PHE 0.018 0.002 PHE B 153 TRP 0.010 0.001 TRP K 108 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00451 (16175) covalent geometry : angle 0.58198 (22122) SS BOND : bond 0.00234 ( 14) SS BOND : angle 1.08168 ( 28) hydrogen bonds : bond 0.06846 ( 383) hydrogen bonds : angle 4.35077 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 40 ARG cc_start: 0.8694 (tpp80) cc_final: 0.8141 (tpt170) REVERT: I 107 TYR cc_start: 0.8844 (t80) cc_final: 0.8331 (t80) REVERT: J 40 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7876 (tpt170) REVERT: J 46 GLU cc_start: 0.9112 (tp30) cc_final: 0.8867 (tp30) REVERT: J 102 ARG cc_start: 0.8277 (mmp80) cc_final: 0.7946 (mmm160) REVERT: J 107 TYR cc_start: 0.9058 (t80) cc_final: 0.8653 (t80) REVERT: N 2 ILE cc_start: 0.9140 (mt) cc_final: 0.8930 (mm) REVERT: N 21 MET cc_start: 0.8795 (pmm) cc_final: 0.8414 (pmm) REVERT: N 32 MET cc_start: 0.8770 (mmm) cc_final: 0.8112 (mmm) REVERT: K 3 GLN cc_start: 0.8951 (mp10) cc_final: 0.8552 (mp10) REVERT: K 46 GLU cc_start: 0.8811 (tp30) cc_final: 0.8577 (tp30) REVERT: O 11 MET cc_start: 0.7949 (pmm) cc_final: 0.7735 (pmm) REVERT: A 82 ASP cc_start: 0.9458 (t0) cc_final: 0.9079 (t0) REVERT: A 516 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: A 601 TYR cc_start: 0.7030 (p90) cc_final: 0.6814 (p90) REVERT: B 482 CYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8951 (t) REVERT: B 528 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: B 601 TYR cc_start: 0.7280 (p90) cc_final: 0.7069 (p90) REVERT: C 559 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7463 (p90) outliers start: 50 outliers final: 30 residues processed: 179 average time/residue: 0.1158 time to fit residues: 31.1400 Evaluate side-chains 171 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 93 TYR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 322 TRP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 111 optimal weight: 0.0030 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 217 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.073789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052138 restraints weight = 78572.194| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.67 r_work: 0.2951 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16189 Z= 0.094 Angle : 0.507 9.572 22150 Z= 0.263 Chirality : 0.042 0.148 2485 Planarity : 0.003 0.054 2897 Dihedral : 3.822 56.870 2465 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.63 % Allowed : 24.30 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 2244 helix: 3.71 (0.36), residues: 213 sheet: 0.41 (0.24), residues: 549 loop : -2.11 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 44 TYR 0.015 0.001 TYR C 117 PHE 0.017 0.001 PHE I 29 TRP 0.010 0.001 TRP B 403 HIS 0.001 0.000 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00197 (16175) covalent geometry : angle 0.50676 (22122) SS BOND : bond 0.00154 ( 14) SS BOND : angle 0.77176 ( 28) hydrogen bonds : bond 0.04833 ( 383) hydrogen bonds : angle 3.85678 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: I 37 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8908 (p) REVERT: I 40 ARG cc_start: 0.8517 (tpp80) cc_final: 0.7885 (tpt170) REVERT: I 102 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7447 (mmm160) REVERT: I 107 TYR cc_start: 0.8794 (t80) cc_final: 0.8355 (t80) REVERT: M 93 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4889 (m-80) REVERT: J 40 ARG cc_start: 0.8433 (tpp80) cc_final: 0.7858 (tpt170) REVERT: J 46 GLU cc_start: 0.9093 (tp30) cc_final: 0.8839 (tp30) REVERT: J 102 ARG cc_start: 0.8312 (mmp80) cc_final: 0.7972 (tpp80) REVERT: J 107 TYR cc_start: 0.9046 (t80) cc_final: 0.8709 (t80) REVERT: N 21 MET cc_start: 0.8808 (pmm) cc_final: 0.8448 (pmm) REVERT: N 32 MET cc_start: 0.8655 (mmm) cc_final: 0.8169 (mmm) REVERT: N 33 TYR cc_start: 0.8717 (m-80) cc_final: 0.8193 (m-80) REVERT: K 3 GLN cc_start: 0.8968 (mp10) cc_final: 0.8383 (mp10) REVERT: K 102 ARG cc_start: 0.8232 (mmp80) cc_final: 0.7903 (tpp80) REVERT: O 11 MET cc_start: 0.8070 (pmm) cc_final: 0.7855 (pmm) REVERT: O 38 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8083 (mmtm) REVERT: A 82 ASP cc_start: 0.9440 (t0) cc_final: 0.9027 (t0) REVERT: A 238 ASN cc_start: 0.8013 (p0) cc_final: 0.7720 (t0) REVERT: A 516 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8716 (m-10) REVERT: A 601 TYR cc_start: 0.6971 (p90) cc_final: 0.6748 (p90) REVERT: B 601 TYR cc_start: 0.7162 (p90) cc_final: 0.6957 (p90) REVERT: C 238 ASN cc_start: 0.7896 (p0) cc_final: 0.7691 (t0) REVERT: C 559 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7420 (p90) outliers start: 33 outliers final: 19 residues processed: 161 average time/residue: 0.1291 time to fit residues: 30.7870 Evaluate side-chains 156 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 101 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 72 optimal weight: 0.0870 chunk 51 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.070734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048749 restraints weight = 80724.250| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.56 r_work: 0.2844 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.8016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16189 Z= 0.220 Angle : 0.597 11.375 22150 Z= 0.318 Chirality : 0.044 0.202 2485 Planarity : 0.003 0.061 2897 Dihedral : 4.541 58.962 2465 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.67 % Allowed : 23.27 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2244 helix: 3.19 (0.37), residues: 216 sheet: 0.20 (0.22), residues: 600 loop : -2.29 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 40 TYR 0.021 0.002 TYR C 117 PHE 0.018 0.002 PHE A 153 TRP 0.011 0.001 TRP K 108 HIS 0.005 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00505 (16175) covalent geometry : angle 0.59627 (22122) SS BOND : bond 0.00246 ( 14) SS BOND : angle 1.10746 ( 28) hydrogen bonds : bond 0.07069 ( 383) hydrogen bonds : angle 4.34105 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: I 40 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8328 (tpt170) REVERT: M 93 TYR cc_start: 0.5599 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: J 40 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7877 (tpt170) REVERT: J 46 GLU cc_start: 0.9110 (tp30) cc_final: 0.8851 (tp30) REVERT: J 102 ARG cc_start: 0.8497 (mmp80) cc_final: 0.8194 (mmm160) REVERT: J 107 TYR cc_start: 0.9043 (t80) cc_final: 0.8470 (t80) REVERT: N 2 ILE cc_start: 0.9221 (mt) cc_final: 0.9008 (mm) REVERT: N 21 MET cc_start: 0.8774 (pmm) cc_final: 0.8232 (pmm) REVERT: N 32 MET cc_start: 0.8767 (mmm) cc_final: 0.8362 (mmm) REVERT: N 33 TYR cc_start: 0.8933 (m-80) cc_final: 0.8366 (m-80) REVERT: K 3 GLN cc_start: 0.9024 (mp10) cc_final: 0.8404 (mp10) REVERT: A 82 ASP cc_start: 0.9445 (t0) cc_final: 0.9104 (t0) REVERT: A 516 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8803 (m-10) REVERT: B 482 CYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9068 (t) REVERT: B 528 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: C 559 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7358 (p90) REVERT: C 599 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6801 (t80) outliers start: 46 outliers final: 31 residues processed: 167 average time/residue: 0.1379 time to fit residues: 34.1743 Evaluate side-chains 166 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 93 TYR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 322 TRP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.070091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048361 restraints weight = 79056.448| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.55 r_work: 0.2819 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16189 Z= 0.248 Angle : 0.632 11.255 22150 Z= 0.337 Chirality : 0.045 0.208 2485 Planarity : 0.003 0.043 2897 Dihedral : 4.769 57.761 2465 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.43 % Allowed : 23.67 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 2244 helix: 2.53 (0.37), residues: 234 sheet: -0.40 (0.21), residues: 669 loop : -2.35 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 44 TYR 0.022 0.002 TYR C 117 PHE 0.023 0.002 PHE C 153 TRP 0.013 0.001 TRP K 108 HIS 0.003 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00571 (16175) covalent geometry : angle 0.63167 (22122) SS BOND : bond 0.00269 ( 14) SS BOND : angle 1.07549 ( 28) hydrogen bonds : bond 0.06947 ( 383) hydrogen bonds : angle 4.36173 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7437 (tm-30) REVERT: I 37 VAL cc_start: 0.9186 (m) cc_final: 0.8967 (p) REVERT: I 40 ARG cc_start: 0.8555 (tpp80) cc_final: 0.7947 (tpt170) REVERT: M 74 ILE cc_start: 0.8223 (mp) cc_final: 0.7508 (tt) REVERT: M 93 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: J 10 GLU cc_start: 0.7959 (pp20) cc_final: 0.7358 (pm20) REVERT: J 40 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7805 (tpt170) REVERT: J 46 GLU cc_start: 0.9160 (tp30) cc_final: 0.8877 (tp30) REVERT: J 102 ARG cc_start: 0.8533 (mmp80) cc_final: 0.8087 (tpp80) REVERT: J 107 TYR cc_start: 0.9033 (t80) cc_final: 0.8471 (t80) REVERT: N 11 MET cc_start: 0.8040 (pmm) cc_final: 0.7795 (pmm) REVERT: N 21 MET cc_start: 0.8656 (pmm) cc_final: 0.8223 (pmm) REVERT: N 33 TYR cc_start: 0.8917 (m-80) cc_final: 0.8552 (m-80) REVERT: K 3 GLN cc_start: 0.9061 (mp10) cc_final: 0.8781 (mm110) REVERT: A 82 ASP cc_start: 0.9442 (t0) cc_final: 0.9085 (t0) REVERT: A 516 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8805 (m-10) REVERT: A 601 TYR cc_start: 0.7130 (p90) cc_final: 0.6707 (p90) REVERT: B 482 CYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8896 (t) REVERT: B 528 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: C 599 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7212 (t80) outliers start: 43 outliers final: 28 residues processed: 162 average time/residue: 0.1284 time to fit residues: 31.5712 Evaluate side-chains 152 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 322 TRP Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 599 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 153 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.069318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047238 restraints weight = 79414.286| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.63 r_work: 0.2782 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16189 Z= 0.298 Angle : 0.691 11.978 22150 Z= 0.369 Chirality : 0.046 0.228 2485 Planarity : 0.004 0.048 2897 Dihedral : 5.153 57.884 2465 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 3.82 % Allowed : 23.59 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 2244 helix: 2.32 (0.37), residues: 234 sheet: -0.51 (0.21), residues: 666 loop : -2.55 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 116 TYR 0.025 0.002 TYR A 103 PHE 0.027 0.002 PHE C 153 TRP 0.015 0.002 TRP K 108 HIS 0.005 0.001 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00687 (16175) covalent geometry : angle 0.69029 (22122) SS BOND : bond 0.00320 ( 14) SS BOND : angle 1.31253 ( 28) hydrogen bonds : bond 0.07566 ( 383) hydrogen bonds : angle 4.63187 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7593 (tm-30) REVERT: I 40 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8186 (tpt170) REVERT: M 74 ILE cc_start: 0.8466 (mp) cc_final: 0.7890 (tt) REVERT: M 93 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: J 10 GLU cc_start: 0.8361 (pp20) cc_final: 0.7716 (pm20) REVERT: J 40 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8054 (tpt170) REVERT: J 46 GLU cc_start: 0.9228 (tp30) cc_final: 0.8950 (tp30) REVERT: J 102 ARG cc_start: 0.8683 (mmp80) cc_final: 0.8304 (tpp80) REVERT: J 107 TYR cc_start: 0.9065 (t80) cc_final: 0.8492 (t80) REVERT: N 33 TYR cc_start: 0.8959 (m-80) cc_final: 0.8255 (m-80) REVERT: N 74 ILE cc_start: 0.8600 (mp) cc_final: 0.7895 (tt) REVERT: K 3 GLN cc_start: 0.9043 (mp10) cc_final: 0.8832 (mm110) REVERT: K 40 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8359 (tpt170) REVERT: K 107 TYR cc_start: 0.8874 (t80) cc_final: 0.8375 (t80) REVERT: A 82 ASP cc_start: 0.9477 (t0) cc_final: 0.9082 (t0) REVERT: A 516 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8837 (m-10) REVERT: A 601 TYR cc_start: 0.7055 (p90) cc_final: 0.6674 (p90) REVERT: B 482 CYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8915 (t) REVERT: B 528 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: B 599 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 601 TYR cc_start: 0.7109 (p90) cc_final: 0.6746 (p90) REVERT: C 599 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7460 (t80) outliers start: 48 outliers final: 37 residues processed: 159 average time/residue: 0.1217 time to fit residues: 29.9602 Evaluate side-chains 158 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 322 TRP Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 115 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.070633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.048962 restraints weight = 78512.759| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.56 r_work: 0.2842 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.8920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16189 Z= 0.156 Angle : 0.596 12.571 22150 Z= 0.309 Chirality : 0.044 0.176 2485 Planarity : 0.003 0.044 2897 Dihedral : 4.602 55.935 2465 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.95 % Allowed : 24.86 % Favored : 72.19 % 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 are not related in a simple way. whole: -1.86 (0.18), residues: 2244 helix: 2.65 (0.37), residues: 234 sheet: -0.52 (0.22), residues: 648 loop : -2.47 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 44 TYR 0.023 0.001 TYR I 103 PHE 0.016 0.001 PHE I 29 TRP 0.013 0.001 TRP N 90 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00354 (16175) covalent geometry : angle 0.59534 (22122) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.85632 ( 28) hydrogen bonds : bond 0.06047 ( 383) hydrogen bonds : angle 4.20506 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7582 (tm-30) REVERT: I 40 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8257 (tpt170) REVERT: M 74 ILE cc_start: 0.8523 (mp) cc_final: 0.7979 (tt) REVERT: M 93 TYR cc_start: 0.5624 (OUTLIER) cc_final: 0.5204 (m-80) REVERT: J 10 GLU cc_start: 0.8453 (pp20) cc_final: 0.7778 (pp20) REVERT: J 40 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8047 (tpt170) REVERT: J 46 GLU cc_start: 0.9236 (tp30) cc_final: 0.8945 (tp30) REVERT: J 102 ARG cc_start: 0.8701 (mmp80) cc_final: 0.8400 (tpp80) REVERT: J 107 TYR cc_start: 0.9016 (t80) cc_final: 0.8498 (t80) REVERT: N 21 MET cc_start: 0.8539 (pmm) cc_final: 0.8258 (pmm) REVERT: N 33 TYR cc_start: 0.8909 (m-80) cc_final: 0.8146 (m-80) REVERT: N 74 ILE cc_start: 0.8741 (mp) cc_final: 0.8220 (tt) REVERT: K 3 GLN cc_start: 0.9045 (mp10) cc_final: 0.8763 (mm110) REVERT: K 40 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8280 (tpt170) REVERT: K 46 GLU cc_start: 0.9110 (tp30) cc_final: 0.8823 (tp30) REVERT: K 107 TYR cc_start: 0.8820 (t80) cc_final: 0.8339 (t80) REVERT: A 82 ASP cc_start: 0.9457 (t0) cc_final: 0.9074 (t0) REVERT: A 516 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8733 (m-10) REVERT: A 601 TYR cc_start: 0.7058 (p90) cc_final: 0.6674 (p90) REVERT: B 87 CYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8731 (m) REVERT: B 601 TYR cc_start: 0.7028 (p90) cc_final: 0.6624 (p90) REVERT: C 599 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6607 (t80) outliers start: 37 outliers final: 27 residues processed: 148 average time/residue: 0.1223 time to fit residues: 27.9564 Evaluate side-chains 148 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 94 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 109 optimal weight: 30.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.069513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047572 restraints weight = 78393.497| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.60 r_work: 0.2794 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.9188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16189 Z= 0.258 Angle : 0.662 12.892 22150 Z= 0.347 Chirality : 0.045 0.204 2485 Planarity : 0.003 0.047 2897 Dihedral : 4.928 56.914 2465 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 3.27 % Allowed : 24.62 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2244 helix: 2.43 (0.37), residues: 234 sheet: -0.65 (0.21), residues: 648 loop : -2.49 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 44 TYR 0.021 0.002 TYR A 103 PHE 0.023 0.002 PHE B 153 TRP 0.013 0.002 TRP K 108 HIS 0.004 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00594 (16175) covalent geometry : angle 0.66078 (22122) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.13114 ( 28) hydrogen bonds : bond 0.07189 ( 383) hydrogen bonds : angle 4.50509 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7540 (tm-30) REVERT: I 13 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8267 (tpp80) REVERT: I 40 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8167 (tpt170) REVERT: M 74 ILE cc_start: 0.8541 (mp) cc_final: 0.8009 (tt) REVERT: J 10 GLU cc_start: 0.8483 (pp20) cc_final: 0.7908 (pp20) REVERT: J 46 GLU cc_start: 0.9254 (tp30) cc_final: 0.8815 (tp30) REVERT: J 102 ARG cc_start: 0.8688 (mmp80) cc_final: 0.8374 (tpp80) REVERT: J 107 TYR cc_start: 0.9032 (t80) cc_final: 0.8488 (t80) REVERT: N 33 TYR cc_start: 0.8927 (m-80) cc_final: 0.8230 (m-80) REVERT: N 74 ILE cc_start: 0.8784 (mp) cc_final: 0.8217 (tt) REVERT: K 3 GLN cc_start: 0.9044 (mp10) cc_final: 0.8747 (mm110) REVERT: K 40 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8243 (tpt170) REVERT: K 46 GLU cc_start: 0.9146 (tp30) cc_final: 0.8867 (tp30) REVERT: K 102 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8438 (tpp80) REVERT: K 107 TYR cc_start: 0.8842 (t80) cc_final: 0.8327 (t80) REVERT: A 82 ASP cc_start: 0.9475 (t0) cc_final: 0.9069 (t0) REVERT: A 516 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8806 (m-10) REVERT: A 601 TYR cc_start: 0.7056 (p90) cc_final: 0.6685 (p90) REVERT: B 87 CYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8765 (m) REVERT: B 528 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 599 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7067 (t80) REVERT: C 599 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7328 (t80) outliers start: 41 outliers final: 31 residues processed: 154 average time/residue: 0.1367 time to fit residues: 31.1920 Evaluate side-chains 157 residues out of total 2025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain M residue 93 TYR Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain O residue 93 TYR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 599 TYR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 322 TRP Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 125 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 213 optimal weight: 0.0370 chunk 216 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.069336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047224 restraints weight = 77926.673| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.69 r_work: 0.2785 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.9345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16189 Z= 0.267 Angle : 0.671 13.146 22150 Z= 0.353 Chirality : 0.046 0.204 2485 Planarity : 0.004 0.047 2897 Dihedral : 5.030 56.802 2465 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.92 % Favored : 89.04 % Rotamer: Outliers : 3.43 % Allowed : 24.70 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.17), residues: 2244 helix: 2.37 (0.36), residues: 234 sheet: -0.80 (0.22), residues: 636 loop : -2.50 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 44 TYR 0.022 0.002 TYR A 103 PHE 0.025 0.002 PHE C 153 TRP 0.012 0.002 TRP N 90 HIS 0.004 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00615 (16175) covalent geometry : angle 0.67064 (22122) SS BOND : bond 0.00328 ( 14) SS BOND : angle 1.14081 ( 28) hydrogen bonds : bond 0.07117 ( 383) hydrogen bonds : angle 4.55520 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.84 seconds wall clock time: 80 minutes 5.98 seconds (4805.98 seconds total)