Starting phenix.real_space_refine on Fri Jun 28 13:34:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w20_43736/06_2024/8w20_43736.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.110 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 50 5.16 5 C 9462 2.51 5 N 3000 2.21 5 O 2900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15412 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 768 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2091 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1275 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 19, 'TRP:plan': 7, 'ASP:plan': 37, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 547 Chain: "A" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 4279 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 15, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 1073 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 53, 'GLU:plan': 52, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 756 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1125 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 12, 'TRANS': 208} Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 278 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 696 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1115 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 275 Chain: "H" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 728 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2044 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 1029 Unresolved non-hydrogen angles: 1346 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 19, 'TRP:plan': 8, 'ASP:plan': 37, 'PHE:plan': 9, 'GLU:plan': 8, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 580 Chain: "J" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 698 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1112 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 275 Time building chain proxies: 8.68, per 1000 atoms: 0.56 Number of scatterers: 15412 At special positions: 0 Unit cell: (236.04, 239.412, 210.75, 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 50 16.00 O 2900 8.00 N 3000 7.00 C 9462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.11 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 71 " distance=2.10 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 78 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 71 " distance=2.09 Simple disulfide: pdb=" SG CYS G 192 " - pdb=" SG CYS G 222 " distance=2.03 Simple disulfide: pdb=" SG CYS H 78 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 71 " distance=2.08 Simple disulfide: pdb=" SG CYS I 192 " - pdb=" SG CYS I 222 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 71 " distance=2.07 Simple disulfide: pdb=" SG CYS K 192 " - pdb=" SG CYS K 222 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.03 Conformation dependent library (CDL) restraints added in 3.1 seconds 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 31 sheets defined 30.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 81 through 111 Proline residue: A 93 - end of helix removed outlier: 4.055A pdb=" N HIS A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 138 through 157 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 182 through 203 removed outlier: 3.571A pdb=" N THR A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 228 through 335 Processing helix chain 'A' and resid 445 through 595 removed outlier: 3.716A pdb=" N THR A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.817A pdb=" N LYS A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 643 through 664 removed outlier: 3.863A pdb=" N THR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 696 through 709 removed outlier: 3.505A pdb=" N VAL A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 Processing helix chain 'A' and resid 727 through 737 Processing helix chain 'A' and resid 737 through 758 removed outlier: 3.511A pdb=" N GLY A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 783 through 889 Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.551A pdb=" N ALA D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.533A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'H' and resid 54 through 62 removed outlier: 3.538A pdb=" N ALA H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 151 Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 238 through 247 Processing helix chain 'J' and resid 54 through 62 Processing helix chain 'J' and resid 148 through 151 Processing helix chain 'K' and resid 69 through 73 Processing helix chain 'K' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.781A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.508A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.535A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.310A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL C 176 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN C 182 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.607A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 Processing sheet with id=AB1, first strand: chain 'D' and resid 73 through 76 removed outlier: 3.609A pdb=" N CYS D 96 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.755A pdb=" N THR D 126 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU D 162 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS D 124 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 43 through 48 removed outlier: 3.511A pdb=" N GLU E 112 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR E 91 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 138 removed outlier: 7.325A pdb=" N ARG E 137 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY E 212 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 233 " --> pdb=" O ASN E 215 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER E 217 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP E 231 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL E 176 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN E 182 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP E 203 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL E 152 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 212 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN E 202 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU E 210 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS E 204 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.718A pdb=" N CYS F 96 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN F 85 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE F 116 " --> pdb=" O GLN F 85 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET F 87 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.717A pdb=" N THR F 126 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 162 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS F 124 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 43 through 48 removed outlier: 3.517A pdb=" N GLU G 112 " --> pdb=" O ARG G 125 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR G 91 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 137 through 138 removed outlier: 7.317A pdb=" N ARG G 137 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY G 212 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE G 233 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER G 217 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP G 231 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL G 176 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN G 182 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP G 203 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G 152 " --> pdb=" O PRO G 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 200 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.664A pdb=" N CYS H 96 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA H 104 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR H 126 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 162 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS H 124 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP I 203 " --> pdb=" O PRO I 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL I 152 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 200 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN I 182 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL I 176 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP I 231 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER I 217 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE I 233 " --> pdb=" O ASN I 215 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 43 through 48 removed outlier: 3.515A pdb=" N GLU I 112 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR I 91 " --> pdb=" O VAL I 110 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 259 through 262 Processing sheet with id=AC6, first strand: chain 'I' and resid 333 through 334 Processing sheet with id=AC7, first strand: chain 'I' and resid 369 through 369 Processing sheet with id=AC8, first strand: chain 'I' and resid 409 through 413 removed outlier: 3.590A pdb=" N THR I 411 " --> pdb=" O THR I 425 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR I 425 " --> pdb=" O THR I 411 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 485 through 486 Processing sheet with id=AD1, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.608A pdb=" N CYS J 96 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 104 through 106 removed outlier: 6.721A pdb=" N THR J 126 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU J 162 " --> pdb=" O LYS J 124 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS J 124 " --> pdb=" O LEU J 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 43 through 48 removed outlier: 3.532A pdb=" N GLU K 112 " --> pdb=" O ARG K 125 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR K 91 " --> pdb=" O VAL K 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 137 through 138 removed outlier: 7.333A pdb=" N ARG K 137 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY K 212 " --> pdb=" O ARG K 137 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE K 233 " --> pdb=" O ASN K 215 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER K 217 " --> pdb=" O ASP K 231 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP K 231 " --> pdb=" O SER K 217 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 180 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL K 176 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN K 182 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP K 203 " --> pdb=" O PRO K 148 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL K 152 " --> pdb=" O PRO K 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU K 200 " --> pdb=" O VAL K 211 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2867 1.26 - 1.40: 3476 1.40 - 1.55: 9101 1.55 - 1.69: 80 1.69 - 1.83: 70 Bond restraints: 15594 Sorted by residual: bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.235 1.121 0.114 1.30e-02 5.92e+03 7.73e+01 bond pdb=" CA ARG A 234 " pdb=" C ARG A 234 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.26e-02 6.30e+03 5.41e+01 bond pdb=" C LYS D 124 " pdb=" O LYS D 124 " ideal model delta sigma weight residual 1.236 1.169 0.066 1.21e-02 6.83e+03 3.01e+01 bond pdb=" N ASP A 599 " pdb=" CA ASP A 599 " ideal model delta sigma weight residual 1.457 1.491 -0.035 6.40e-03 2.44e+04 2.94e+01 bond pdb=" CA LEU A 638 " pdb=" C LEU A 638 " ideal model delta sigma weight residual 1.524 1.592 -0.068 1.28e-02 6.10e+03 2.78e+01 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.24: 297 104.24 - 111.63: 7343 111.63 - 119.01: 4657 119.01 - 126.40: 9104 126.40 - 133.79: 143 Bond angle restraints: 21544 Sorted by residual: angle pdb=" N TRP A 645 " pdb=" CA TRP A 645 " pdb=" C TRP A 645 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.66e+01 angle pdb=" N ASP A 639 " pdb=" CA ASP A 639 " pdb=" C ASP A 639 " ideal model delta sigma weight residual 111.33 122.89 -11.56 1.21e+00 6.83e-01 9.13e+01 angle pdb=" N VAL A 637 " pdb=" CA VAL A 637 " pdb=" C VAL A 637 " ideal model delta sigma weight residual 111.00 101.46 9.54 1.09e+00 8.42e-01 7.66e+01 angle pdb=" C GLY A 619 " pdb=" N PRO A 620 " pdb=" CA PRO A 620 " ideal model delta sigma weight residual 119.32 128.78 -9.46 1.14e+00 7.69e-01 6.89e+01 angle pdb=" N ALA A 257 " pdb=" CA ALA A 257 " pdb=" C ALA A 257 " ideal model delta sigma weight residual 111.36 102.36 9.00 1.09e+00 8.42e-01 6.81e+01 ... (remaining 21539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8989 16.01 - 32.02: 71 32.02 - 48.02: 33 48.02 - 64.03: 16 64.03 - 80.04: 2 Dihedral angle restraints: 9111 sinusoidal: 1193 harmonic: 7918 Sorted by residual: dihedral pdb=" C TYR J 105 " pdb=" N TYR J 105 " pdb=" CA TYR J 105 " pdb=" CB TYR J 105 " ideal model delta harmonic sigma weight residual -122.60 -103.38 -19.22 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CB CYS K 192 " pdb=" SG CYS K 192 " pdb=" SG CYS K 222 " pdb=" CB CYS K 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.47 -59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.19 -59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2321 0.084 - 0.168: 305 0.168 - 0.253: 22 0.253 - 0.337: 4 0.337 - 0.421: 4 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CA THR A 643 " pdb=" N THR A 643 " pdb=" C THR A 643 " pdb=" CB THR A 643 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LEU A 805 " pdb=" N LEU A 805 " pdb=" C LEU A 805 " pdb=" CB LEU A 805 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CG LEU A 806 " pdb=" CB LEU A 806 " pdb=" CD1 LEU A 806 " pdb=" CD2 LEU A 806 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 2653 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.017 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C VAL A 762 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN A 763 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 638 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU A 638 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU A 638 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 639 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 233 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ALA A 233 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 233 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 234 " 0.019 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4786 2.80 - 3.33: 12849 3.33 - 3.85: 23389 3.85 - 4.38: 22958 4.38 - 4.90: 41184 Nonbonded interactions: 105166 Sorted by model distance: nonbonded pdb=" O VAL A 600 " pdb=" N ALA A 602 " model vdw 2.278 2.520 nonbonded pdb=" CB GLU H 82 " pdb=" OE1 GLN H 85 " model vdw 2.404 3.440 nonbonded pdb=" O TYR F 147 " pdb=" C GLY F 148 " model vdw 2.492 3.270 nonbonded pdb=" O TYR H 147 " pdb=" C GLY H 148 " model vdw 2.501 3.270 nonbonded pdb=" O TYR D 147 " pdb=" C GLY D 148 " model vdw 2.506 3.270 ... (remaining 105161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 56 or (resid 57 through 62 and (name N or name \ CA or name C or name O or name CB )) or (resid 63 through 68 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or na \ me CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 thro \ ugh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 98 or (resid 99 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 161 or (resid 162 through 165 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'D' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 99 or (resid 100 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB )) or resid 114 through 115 or \ (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 123 or (resid 124 through 131 and (name N or name CA or name C or name \ O or name CB )) or (resid 132 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 146 or (resid 147 and (name N or name C \ A or name C or name O or name CB )) or resid 148 or (resid 149 through 150 and ( \ name N or name CA or name C or name O or name CB )) or resid 151 through 161 or \ (resid 162 through 165 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'F' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 57 or (resid 58 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 91 or (resid 92 through 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 136 or (resid 137 through 139 and (nam \ e N or name CA or name C or name O or name CB )) or resid 140 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 161 or (resid 162 through 165 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'H' and (resid 45 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 99 or (resid 100 through 102 and (name N or name CA or name C or name O or nam \ e CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name C \ A or name C or name O or name CB )) or resid 111 through 136 or (resid 137 throu \ gh 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thr \ ough 148 or (resid 149 through 150 and (name N or name CA or name C or name O or \ name CB )) or resid 151 through 161 or (resid 162 through 165 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 64 or (resid 65 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 104 or (resid 105 thr \ ough 110 and (name N or name CA or name C or name O or name CB )) or resid 111 t \ hrough 146 or (resid 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 165)) } ncs_group { reference = (chain 'C' and (resid 30 through 41 or (resid 42 through 48 and (name N or name \ CA or name C or name O or name CB )) or (resid 49 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 63 or (resid 64 throug \ h 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throug \ h 117 or (resid 118 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 190 or (resid 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 504)) selection = (chain 'I' and (resid 30 through 165 or (resid 166 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 504)) } ncs_group { reference = (chain 'E' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = (chain 'G' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 6.800 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.130 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 : 0.008 0.114 15594 Z= 0.530 Angle : 1.339 13.764 21544 Z= 0.946 Chirality : 0.057 0.421 2656 Planarity : 0.005 0.037 3056 Dihedral : 6.792 80.040 3954 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.59 % Favored : 97.16 % Rotamer: Outliers : 0.45 % Allowed : 0.89 % Favored : 98.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2742 helix: 1.64 (0.16), residues: 771 sheet: 1.37 (0.21), residues: 661 loop : 0.09 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP C 64 HIS 0.003 0.001 HIS A 622 PHE 0.013 0.003 PHE F 97 TYR 0.037 0.004 TYR A 640 ARG 0.010 0.001 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7865 (mt0) cc_final: 0.7579 (tm-30) REVERT: A 753 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8396 (mmm-85) REVERT: A 756 GLU cc_start: 0.8829 (tt0) cc_final: 0.7871 (tm-30) REVERT: D 66 LEU cc_start: 0.8618 (mp) cc_final: 0.8396 (mt) REVERT: J 105 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7223 (m-10) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2294 time to fit residues: 58.5950 Evaluate side-chains 108 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 0.1980 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 217 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 251 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15594 Z= 0.205 Angle : 0.532 6.275 21544 Z= 0.299 Chirality : 0.043 0.182 2656 Planarity : 0.004 0.043 3056 Dihedral : 4.099 21.298 2839 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.45 % Allowed : 3.12 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2742 helix: 2.94 (0.16), residues: 802 sheet: 1.06 (0.20), residues: 746 loop : 0.20 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 645 HIS 0.005 0.001 HIS B 72 PHE 0.026 0.002 PHE J 97 TYR 0.015 0.002 TYR B 114 ARG 0.006 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.269 Fit side-chains REVERT: A 222 MET cc_start: 0.8435 (mtp) cc_final: 0.8122 (mtp) REVERT: A 612 MET cc_start: 0.8655 (tpt) cc_final: 0.8439 (tpt) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.1966 time to fit residues: 40.7595 Evaluate side-chains 91 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 139 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 224 optimal weight: 30.0000 chunk 249 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 622 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 15594 Z= 0.522 Angle : 0.785 12.264 21544 Z= 0.447 Chirality : 0.049 0.283 2656 Planarity : 0.006 0.072 3056 Dihedral : 5.112 30.295 2839 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.89 % Allowed : 6.68 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2742 helix: 2.39 (0.17), residues: 789 sheet: 0.45 (0.20), residues: 695 loop : -0.27 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP I 161 HIS 0.019 0.004 HIS H 72 PHE 0.068 0.005 PHE B 97 TYR 0.043 0.004 TYR D 105 ARG 0.010 0.002 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: C 52 TYR cc_start: 0.8326 (t80) cc_final: 0.8047 (t80) REVERT: A 787 MET cc_start: 0.8495 (ttt) cc_final: 0.8265 (ttm) REVERT: D 75 MET cc_start: 0.7522 (ttp) cc_final: 0.7259 (ttt) REVERT: H 105 TYR cc_start: 0.8314 (p90) cc_final: 0.8028 (p90) REVERT: J 75 MET cc_start: 0.9047 (ttm) cc_final: 0.8743 (ttm) REVERT: J 147 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7485 (m-80) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.1688 time to fit residues: 29.3902 Evaluate side-chains 80 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 248 optimal weight: 0.8980 chunk 189 optimal weight: 50.0000 chunk 130 optimal weight: 0.7980 chunk 27 optimal weight: 30.0000 chunk 120 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 252 optimal weight: 10.0000 chunk 267 optimal weight: 50.0000 chunk 132 optimal weight: 0.6980 chunk 239 optimal weight: 50.0000 chunk 72 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15594 Z= 0.184 Angle : 0.485 5.626 21544 Z= 0.273 Chirality : 0.042 0.130 2656 Planarity : 0.004 0.056 3056 Dihedral : 3.919 21.479 2839 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2742 helix: 3.29 (0.16), residues: 793 sheet: 0.44 (0.19), residues: 736 loop : -0.03 (0.19), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 117 HIS 0.010 0.002 HIS A 146 PHE 0.018 0.002 PHE D 95 TYR 0.016 0.001 TYR J 147 ARG 0.003 0.000 ARG A 790 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8554 (ttt) cc_final: 0.8334 (ttt) REVERT: D 75 MET cc_start: 0.7804 (ttp) cc_final: 0.7604 (ttt) REVERT: H 105 TYR cc_start: 0.8149 (p90) cc_final: 0.7874 (p90) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1887 time to fit residues: 34.6939 Evaluate side-chains 85 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 222 optimal weight: 30.0000 chunk 151 optimal weight: 50.0000 chunk 3 optimal weight: 0.6980 chunk 199 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 228 optimal weight: 30.0000 chunk 185 optimal weight: 50.0000 chunk 0 optimal weight: 3.9990 chunk 136 optimal weight: 0.0060 chunk 240 optimal weight: 50.0000 chunk 67 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15594 Z= 0.211 Angle : 0.494 5.852 21544 Z= 0.276 Chirality : 0.042 0.139 2656 Planarity : 0.004 0.056 3056 Dihedral : 3.771 20.307 2839 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2742 helix: 3.49 (0.16), residues: 793 sheet: 0.35 (0.19), residues: 733 loop : 0.04 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 117 HIS 0.009 0.002 HIS B 72 PHE 0.018 0.002 PHE B 97 TYR 0.018 0.002 TYR B 114 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.566 Fit side-chains REVERT: C 42 PHE cc_start: 0.7548 (p90) cc_final: 0.7210 (p90) REVERT: A 645 TRP cc_start: 0.7529 (t-100) cc_final: 0.7290 (t-100) REVERT: A 787 MET cc_start: 0.7952 (ttt) cc_final: 0.7676 (ttm) REVERT: D 75 MET cc_start: 0.7895 (ttp) cc_final: 0.7643 (ttt) REVERT: H 87 MET cc_start: 0.7077 (mtm) cc_final: 0.6781 (mtp) REVERT: H 105 TYR cc_start: 0.8141 (p90) cc_final: 0.7880 (p90) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1785 time to fit residues: 28.4386 Evaluate side-chains 78 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 90 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 52 optimal weight: 0.0470 chunk 157 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 268 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 22 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 overall best weight: 2.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 15594 Z= 0.431 Angle : 0.665 9.000 21544 Z= 0.377 Chirality : 0.046 0.186 2656 Planarity : 0.005 0.073 3056 Dihedral : 4.696 29.654 2839 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2742 helix: 2.93 (0.17), residues: 785 sheet: -0.02 (0.20), residues: 700 loop : -0.24 (0.19), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 117 HIS 0.013 0.004 HIS B 72 PHE 0.054 0.004 PHE B 97 TYR 0.039 0.004 TYR H 114 ARG 0.005 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8677 (ttt) cc_final: 0.8236 (ttt) REVERT: D 75 MET cc_start: 0.8016 (ttp) cc_final: 0.7629 (ttt) REVERT: H 87 MET cc_start: 0.7773 (mtm) cc_final: 0.7567 (mtp) REVERT: H 105 TYR cc_start: 0.8284 (p90) cc_final: 0.8044 (p90) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1796 time to fit residues: 27.7157 Evaluate side-chains 71 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 152 optimal weight: 40.0000 chunk 195 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.216 15594 Z= 1.003 Angle : 1.123 14.966 21544 Z= 0.638 Chirality : 0.058 0.347 2656 Planarity : 0.009 0.105 3056 Dihedral : 6.883 35.988 2839 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.72 % Favored : 91.25 % Rotamer: Outliers : 0.45 % Allowed : 6.01 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2742 helix: 0.07 (0.18), residues: 777 sheet: -0.78 (0.20), residues: 661 loop : -1.22 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.006 TRP B 117 HIS 0.023 0.007 HIS D 72 PHE 0.074 0.009 PHE B 97 TYR 0.073 0.007 TYR H 114 ARG 0.015 0.002 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8771 (ttt) cc_final: 0.8407 (ttt) REVERT: D 75 MET cc_start: 0.8065 (ttp) cc_final: 0.7617 (ttt) outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.1895 time to fit residues: 28.2057 Evaluate side-chains 74 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 165 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 80 optimal weight: 50.0000 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 169 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 209 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15594 Z= 0.207 Angle : 0.533 6.439 21544 Z= 0.301 Chirality : 0.043 0.175 2656 Planarity : 0.005 0.062 3056 Dihedral : 4.701 28.935 2839 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2742 helix: 2.45 (0.17), residues: 784 sheet: -0.43 (0.20), residues: 689 loop : -0.77 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 117 HIS 0.009 0.002 HIS B 72 PHE 0.023 0.002 PHE D 95 TYR 0.017 0.002 TYR A 640 ARG 0.003 0.001 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: D 75 MET cc_start: 0.7941 (ttp) cc_final: 0.7543 (ttt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1705 time to fit residues: 28.0296 Evaluate side-chains 78 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 50.0000 chunk 255 optimal weight: 0.9990 chunk 233 optimal weight: 50.0000 chunk 248 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 235 optimal weight: 50.0000 chunk 247 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 15594 Z= 0.438 Angle : 0.676 9.467 21544 Z= 0.382 Chirality : 0.046 0.191 2656 Planarity : 0.006 0.073 3056 Dihedral : 5.081 33.720 2839 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2742 helix: 2.33 (0.18), residues: 783 sheet: -0.55 (0.20), residues: 686 loop : -0.86 (0.19), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP H 117 HIS 0.016 0.004 HIS B 72 PHE 0.038 0.004 PHE D 95 TYR 0.048 0.003 TYR H 114 ARG 0.007 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8622 (ttt) cc_final: 0.8261 (ttt) REVERT: D 75 MET cc_start: 0.8055 (ttp) cc_final: 0.7730 (ttt) REVERT: H 87 MET cc_start: 0.7531 (mtm) cc_final: 0.7323 (mtp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1936 time to fit residues: 27.8792 Evaluate side-chains 69 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 163 optimal weight: 0.6980 chunk 263 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 chunk 182 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 253 optimal weight: 0.0370 chunk 219 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15594 Z= 0.181 Angle : 0.485 6.650 21544 Z= 0.271 Chirality : 0.042 0.143 2656 Planarity : 0.005 0.056 3056 Dihedral : 4.138 26.436 2839 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2742 helix: 3.39 (0.17), residues: 783 sheet: -0.47 (0.20), residues: 720 loop : -0.49 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 117 HIS 0.008 0.002 HIS B 72 PHE 0.021 0.002 PHE D 95 TYR 0.014 0.001 TYR D 105 ARG 0.002 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: B 117 TRP cc_start: 0.8726 (m100) cc_final: 0.6290 (m-10) REVERT: C 42 PHE cc_start: 0.7529 (p90) cc_final: 0.7094 (p90) REVERT: D 75 MET cc_start: 0.8017 (ttp) cc_final: 0.7594 (ttt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1908 time to fit residues: 30.2090 Evaluate side-chains 78 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 20.0000 chunk 234 optimal weight: 50.0000 chunk 67 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 226 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.163911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139976 restraints weight = 40508.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132515 restraints weight = 57637.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129230 restraints weight = 61271.804| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 15594 Z= 0.544 Angle : 0.740 10.011 21544 Z= 0.419 Chirality : 0.048 0.239 2656 Planarity : 0.006 0.073 3056 Dihedral : 5.171 36.240 2839 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2742 helix: 2.50 (0.18), residues: 781 sheet: -0.74 (0.20), residues: 714 loop : -0.77 (0.19), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.004 TRP B 117 HIS 0.020 0.004 HIS B 72 PHE 0.051 0.005 PHE B 95 TYR 0.054 0.004 TYR H 114 ARG 0.010 0.001 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.55 seconds wall clock time: 42 minutes 30.85 seconds (2550.85 seconds total)