Starting phenix.real_space_refine on Fri Aug 7 04:56:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.map" model { file = "/net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9swk_55311/08_2026/9swk_55311.cif" } resolution = 3.57 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= 0.002 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 123 5.16 5 C 11942 2.51 5 N 3398 2.21 5 O 3714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19177 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3569 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 472} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3616 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 472} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3622 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 472} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 958 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 958 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 958 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1804 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Chain: "H" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1804 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Chain: "I" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1804 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.83, per 1000 atoms: 0.20 Number of scatterers: 19177 At special positions: 0 Unit cell: (160.051, 167.554, 136.71, 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 123 16.00 O 3714 8.00 N 3398 7.00 C 11942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 290 " distance=2.04 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 338 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 338 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 65 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 63 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 65 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 186 " - pdb=" SG CYS G 290 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 338 " distance=2.02 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 186 " - pdb=" SG CYS H 290 " distance=2.03 Simple disulfide: pdb=" SG CYS H 307 " - pdb=" SG CYS H 338 " distance=2.03 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 30 " distance=2.02 Simple disulfide: pdb=" SG CYS I 186 " - pdb=" SG CYS I 290 " distance=2.03 Simple disulfide: pdb=" SG CYS I 307 " - pdb=" SG CYS I 338 " distance=2.02 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 154 " " NAG B 501 " - " ASN B 154 " " NAG C 501 " - " ASN C 154 " " NAG G 501 " - " ASN G 154 " " NAG H 501 " - " ASN H 154 " " NAG I 501 " - " ASN I 154 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 799.0 milliseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4710 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 53 sheets defined 19.1% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 237 through 240 removed outlier: 3.804A pdb=" N ARG A 240 " --> pdb=" O ASN A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.570A pdb=" N LEU A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 421 removed outlier: 3.648A pdb=" N VAL A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 449 removed outlier: 5.597A pdb=" N GLY A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 470 removed outlier: 3.891A pdb=" N ASN A 470 " --> pdb=" O TRP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 476 through 492 removed outlier: 4.019A pdb=" N PHE A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.842A pdb=" N THR B 4 " --> pdb=" O SER B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.832A pdb=" N HIS B 86 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.518A pdb=" N ARG B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 241 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 242 " --> pdb=" O GLU B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 399 through 420 removed outlier: 3.626A pdb=" N PHE B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 439 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 470 removed outlier: 3.762A pdb=" N ASN B 470 " --> pdb=" O TRP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.980A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.848A pdb=" N THR C 4 " --> pdb=" O SER C 1 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.535A pdb=" N HIS C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.859A pdb=" N ASN C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS C 104 " --> pdb=" O TRP C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 237 through 240 removed outlier: 3.568A pdb=" N ARG C 240 " --> pdb=" O ASN C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 240' Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 397 through 416 Processing helix chain 'C' and resid 425 through 449 removed outlier: 5.497A pdb=" N GLY C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 removed outlier: 3.709A pdb=" N LYS C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 492 removed outlier: 4.064A pdb=" N LEU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 127 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.845A pdb=" N ALA E 19 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.949A pdb=" N LEU E 117 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR E 118 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 147 through 158 Processing helix chain 'F' and resid 15 through 19 removed outlier: 3.537A pdb=" N ALA F 19 " --> pdb=" O GLY F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.957A pdb=" N HIS F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.527A pdb=" N GLU F 143 " --> pdb=" O TRP F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.654A pdb=" N ALA F 150 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 5 removed outlier: 3.506A pdb=" N THR G 4 " --> pdb=" O SER G 1 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 5 " --> pdb=" O ARG G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1 through 5' Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'I' and resid 1 through 5 removed outlier: 3.711A pdb=" N THR I 4 " --> pdb=" O SER I 1 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.990A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 140 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE A 48 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 138 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.990A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 50 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26 removed outlier: 3.691A pdb=" N LEU A 185 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 183 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLY A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.690A pdb=" N ARG A 57 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.557A pdb=" N ALA A 120 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 99 removed outlier: 3.581A pdb=" N ALA A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU D 48 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA A 72 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N VAL D 50 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP D 43 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL D 71 " --> pdb=" O CYS D 49 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR D 10 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU D 74 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE D 12 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY D 76 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 99 removed outlier: 3.581A pdb=" N ALA A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU D 48 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA A 72 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N VAL D 50 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 11.728A pdb=" N CYS D 63 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU D 48 " --> pdb=" O CYS D 63 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS D 65 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL D 50 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 64 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 21 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA9, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 345 removed outlier: 4.261A pdb=" N ILE A 383 " --> pdb=" O HIS A 390 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS A 390 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 385 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 9 through 13 removed outlier: 7.223A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 12 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 43 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 144 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU B 45 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS B 142 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 47 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 13 removed outlier: 7.223A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR B 34 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 12 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA B 35 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE B 48 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 20 through 26 removed outlier: 3.680A pdb=" N ARG B 187 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 291 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 183 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.605A pdb=" N THR B 128 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU B 58 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY B 129 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 54 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 98 removed outlier: 6.847A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 15.989A pdb=" N LYS B 64 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASP E 42 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER B 66 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 44 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 46 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU E 48 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA B 72 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N VAL E 50 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 43 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL E 71 " --> pdb=" O CYS E 49 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY E 76 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 98 removed outlier: 6.847A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 15.989A pdb=" N LYS B 64 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ASP E 42 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER B 66 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 44 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 46 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU E 48 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA B 72 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N VAL E 50 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N CYS E 63 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLU E 48 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS E 65 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL E 50 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 29 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 313 through 320 removed outlier: 6.253A pdb=" N GLU B 329 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA B 317 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B 327 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AC1, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.785A pdb=" N GLN B 394 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 9 through 14 Processing sheet with id=AC3, first strand: chain 'C' and resid 20 through 22 removed outlier: 4.099A pdb=" N SER C 183 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 20 through 22 removed outlier: 4.099A pdb=" N SER C 183 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS C 296 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 165 removed outlier: 3.959A pdb=" N ALA C 47 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS C 142 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU C 45 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.987A pdb=" N TYR C 59 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AC9, first strand: chain 'C' and resid 90 through 99 removed outlier: 4.378A pdb=" N GLU F 48 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA C 72 " --> pdb=" O GLU F 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 197 through 198 Processing sheet with id=AD2, first strand: chain 'C' and resid 242 through 244 Processing sheet with id=AD3, first strand: chain 'C' and resid 313 through 320 removed outlier: 6.761A pdb=" N GLU C 329 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA C 317 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C 356 " --> pdb=" O GLN C 375 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AD5, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.556A pdb=" N ILE C 382 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 385 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.757A pdb=" N THR F 29 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 66 " --> pdb=" O THR F 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 12 removed outlier: 7.385A pdb=" N ASP G 10 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR G 140 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE G 48 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL G 138 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 12 removed outlier: 7.385A pdb=" N ASP G 10 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE G 48 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 281 " --> pdb=" O GLN G 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 23 through 25 Processing sheet with id=AE1, first strand: chain 'G' and resid 171 through 175 Processing sheet with id=AE2, first strand: chain 'G' and resid 312 through 320 removed outlier: 6.544A pdb=" N LYS G 315 " --> pdb=" O THR G 331 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR G 331 " --> pdb=" O LYS G 315 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA G 317 " --> pdb=" O GLU G 329 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU G 329 " --> pdb=" O ALA G 317 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 338 through 339 Processing sheet with id=AE4, first strand: chain 'G' and resid 342 through 346 removed outlier: 3.871A pdb=" N GLY G 379 " --> pdb=" O GLN G 394 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 385 " --> pdb=" O LEU G 388 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.560A pdb=" N VAL H 12 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR H 140 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE H 48 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL H 138 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.560A pdb=" N VAL H 12 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE H 48 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AE8, first strand: chain 'H' and resid 20 through 22 removed outlier: 3.867A pdb=" N ARG H 187 " --> pdb=" O THR H 289 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 172 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 312 through 320 removed outlier: 6.468A pdb=" N LYS H 315 " --> pdb=" O THR H 331 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR H 331 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA H 317 " --> pdb=" O GLU H 329 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU H 329 " --> pdb=" O ALA H 317 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 338 through 339 Processing sheet with id=AF2, first strand: chain 'H' and resid 342 through 346 removed outlier: 3.584A pdb=" N GLY H 379 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H 394 " --> pdb=" O GLY H 379 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 9 through 13 removed outlier: 7.215A pdb=" N ASP I 10 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR I 34 " --> pdb=" O ASP I 10 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 12 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU I 45 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS I 142 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 47 " --> pdb=" O THR I 140 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 13 removed outlier: 7.215A pdb=" N ASP I 10 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR I 34 " --> pdb=" O ASP I 10 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL I 12 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR I 281 " --> pdb=" O GLN I 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 20 through 26 removed outlier: 3.742A pdb=" N VAL I 182 " --> pdb=" O LEU I 174 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 312 through 320 removed outlier: 6.637A pdb=" N GLU I 329 " --> pdb=" O LYS I 315 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA I 317 " --> pdb=" O VAL I 327 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL I 327 " --> pdb=" O ALA I 317 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 338 through 339 Processing sheet with id=AF8, first strand: chain 'I' and resid 342 through 346 removed outlier: 3.701A pdb=" N GLN I 394 " --> pdb=" O GLY I 379 " (cutoff:3.500A) 753 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6477 1.35 - 1.47: 4595 1.47 - 1.60: 8279 1.60 - 1.73: 0 1.73 - 1.86: 174 Bond restraints: 19525 Sorted by residual: bond pdb=" CB CYS D 30 " pdb=" SG CYS D 30 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" CB VAL E 31 " pdb=" CG1 VAL E 31 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" CE1 TYR B 59 " pdb=" CZ TYR B 59 " ideal model delta sigma weight residual 1.378 1.341 0.037 2.40e-02 1.74e+03 2.33e+00 bond pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.25e+00 ... (remaining 19520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 26241 2.20 - 4.39: 253 4.39 - 6.59: 15 6.59 - 8.78: 3 8.78 - 10.98: 1 Bond angle restraints: 26513 Sorted by residual: angle pdb=" CA CYS D 30 " pdb=" CB CYS D 30 " pdb=" SG CYS D 30 " ideal model delta sigma weight residual 114.40 125.38 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C VAL B 250 " pdb=" N LYS B 251 " pdb=" CA LYS B 251 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA CYS F 65 " pdb=" CB CYS F 65 " pdb=" SG CYS F 65 " ideal model delta sigma weight residual 114.40 122.96 -8.56 2.30e+00 1.89e-01 1.39e+01 angle pdb=" C HIS C 104 " pdb=" N CYS C 105 " pdb=" CA CYS C 105 " ideal model delta sigma weight residual 121.94 115.73 6.21 1.76e+00 3.23e-01 1.25e+01 angle pdb=" N CYS F 65 " pdb=" CA CYS F 65 " pdb=" C CYS F 65 " ideal model delta sigma weight residual 107.88 111.97 -4.09 1.41e+00 5.03e-01 8.42e+00 ... (remaining 26508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10636 17.83 - 35.66: 877 35.66 - 53.49: 157 53.49 - 71.32: 37 71.32 - 89.15: 11 Dihedral angle restraints: 11718 sinusoidal: 4359 harmonic: 7359 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.75 -85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS D 41 " pdb=" SG CYS D 41 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -168.28 82.28 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS B 3 " pdb=" SG CYS B 3 " pdb=" SG CYS B 30 " pdb=" CB CYS B 30 " ideal model delta sinusoidal sigma weight residual 93.00 170.15 -77.15 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 11715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2372 0.050 - 0.101: 565 0.101 - 0.151: 137 0.151 - 0.202: 5 0.202 - 0.252: 3 Chirality restraints: 3082 Sorted by residual: chirality pdb=" CB ILE B 199 " pdb=" CA ILE B 199 " pdb=" CG1 ILE B 199 " pdb=" CG2 ILE B 199 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA HIS C 104 " pdb=" N HIS C 104 " pdb=" C HIS C 104 " pdb=" CB HIS C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 154 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3079 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 246 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO B 247 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 281 " 0.005 2.00e-02 2.50e+03 1.04e-02 2.14e+00 pdb=" CG TYR B 281 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 281 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 281 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 281 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 281 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 64 " -0.014 2.00e-02 2.50e+03 1.08e-02 2.05e+00 pdb=" CG PHE D 64 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE D 64 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 64 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 64 " -0.009 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 361 2.69 - 3.24: 17484 3.24 - 3.79: 27290 3.79 - 4.35: 34427 4.35 - 4.90: 60975 Nonbonded interactions: 140537 Sorted by model distance: nonbonded pdb=" OG SER I 321 " pdb=" OG1 THR I 325 " model vdw 2.135 3.040 nonbonded pdb=" OG SER E 39 " pdb=" O CYS E 78 " model vdw 2.208 3.040 nonbonded pdb=" O CYS H 338 " pdb=" OG1 THR H 363 " model vdw 2.212 3.040 nonbonded pdb=" O GLU A 411 " pdb=" OG1 THR A 414 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 321 " pdb=" OG1 THR B 325 " model vdw 2.227 3.040 ... (remaining 140532 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' selection = (chain 'B' and (resid 1 through 396 or (resid 397 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 or (resid 401 through 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 or (resid 41 \ 0 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 440 or (resid 441 and (name N or name CA or name C or name O or name \ CB )) or resid 442 through 501)) selection = (chain 'C' and (resid 1 through 396 or (resid 397 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 or (resid 401 through 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 or (resid 41 \ 0 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 440 or (resid 441 and (name N or name CA or name C or name O or name \ CB )) or (resid 442 through 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 501)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.210 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.005 0.059 19567 Z= 0.215 Angle : 0.579 10.975 26603 Z= 0.310 Chirality : 0.046 0.252 3082 Planarity : 0.003 0.055 3426 Dihedral : 13.187 89.147 6900 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.32 (0.17), residues: 2568 helix: 2.58 (0.27), residues: 405 sheet: -0.80 (0.18), residues: 836 loop : -0.63 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 187 TYR 0.024 0.002 TYR B 281 PHE 0.023 0.002 PHE D 64 TRP 0.016 0.002 TRP C 213 HIS 0.011 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (19525) covalent geometry : angle 0.56894 / 0.31 (26513) SS BOND : bond 0.00598 / 0.41 ( 36) SS BOND : angle 2.03629 / 1.47 ( 72) hydrogen bonds : bond 0.22306 / 15.48 ( 695) hydrogen bonds : angle 9.03390 / 6.27 ( 2016) link_NAG-ASN : bond 0.00204 / 0.10 ( 6) link_NAG-ASN : angle 1.30271 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8344 (mmm) cc_final: 0.7901 (mmm) REVERT: A 132 TYR cc_start: 0.8411 (m-80) cc_final: 0.8044 (m-80) REVERT: A 142 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8269 (mmtm) REVERT: A 167 ILE cc_start: 0.8954 (tt) cc_final: 0.8738 (tt) REVERT: B 67 ASP cc_start: 0.8072 (t0) cc_final: 0.7737 (t0) REVERT: B 105 CYS cc_start: 0.4332 (m) cc_final: 0.4099 (m) REVERT: B 291 GLU cc_start: 0.7573 (pm20) cc_final: 0.7307 (pt0) REVERT: C 284 LYS cc_start: 0.8530 (tppt) cc_final: 0.8290 (tppt) REVERT: F 18 ASP cc_start: 0.8367 (t70) cc_final: 0.8049 (t70) REVERT: G 161 LYS cc_start: 0.7365 (mmtp) cc_final: 0.7161 (mmtm) REVERT: G 367 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.7182 (p0) outliers start: 2 outliers final: 0 residues processed: 338 average time/residue: 0.1133 time to fit residues: 61.1992 Evaluate side-chains 290 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 367 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.1980 chunk 111 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN B 375 GLN C 236 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 54 GLN I 367 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.201847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.180813 restraints weight = 19746.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.179744 restraints weight = 34322.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.178898 restraints weight = 31114.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.176603 restraints weight = 32535.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.174739 restraints weight = 39559.447| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19567 Z= 0.126 Angle : 0.543 13.100 26603 Z= 0.290 Chirality : 0.044 0.191 3082 Planarity : 0.003 0.059 3426 Dihedral : 4.381 24.165 2872 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 1.46 % Allowed : 10.80 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.11 (0.17), residues: 2568 helix: 2.97 (0.27), residues: 398 sheet: -0.64 (0.18), residues: 859 loop : -0.58 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 77 TYR 0.017 0.001 TYR C 139 PHE 0.014 0.001 PHE D 64 TRP 0.010 0.001 TRP B 227 HIS 0.005 0.001 HIS H 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19525) covalent geometry : angle 0.53578 / 0.29 (26513) SS BOND : bond 0.00581 / 0.40 ( 36) SS BOND : angle 1.70861 / 1.32 ( 72) hydrogen bonds : bond 0.03812 / 2.67 ( 695) hydrogen bonds : angle 5.85820 / 4.02 ( 2016) link_NAG-ASN : bond 0.00234 / 0.12 ( 6) link_NAG-ASN : angle 1.17399 / 0.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.8213 (mmm) cc_final: 0.7655 (mmm) REVERT: A 132 TYR cc_start: 0.8482 (m-80) cc_final: 0.8117 (m-80) REVERT: B 67 ASP cc_start: 0.8154 (t0) cc_final: 0.7898 (t0) REVERT: C 276 ILE cc_start: 0.8207 (mm) cc_final: 0.7953 (mt) REVERT: C 296 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7450 (tttp) REVERT: F 18 ASP cc_start: 0.8129 (t70) cc_final: 0.7902 (t0) REVERT: G 367 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7210 (p0) REVERT: H 41 MET cc_start: 0.7501 (mmt) cc_final: 0.7105 (mmt) REVERT: H 374 MET cc_start: 0.7931 (mtm) cc_final: 0.7722 (mtm) REVERT: I 174 LEU cc_start: 0.8797 (mp) cc_final: 0.8570 (mt) outliers start: 28 outliers final: 19 residues processed: 305 average time/residue: 0.1143 time to fit residues: 55.9802 Evaluate side-chains 287 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 236 ASN A 347 HIS B 135 ASN B 237 ASN C 52 ASN E 27 ASN I 367 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.191745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.171608 restraints weight = 20137.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.169921 restraints weight = 34048.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.168727 restraints weight = 32096.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.166925 restraints weight = 33271.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.164911 restraints weight = 37267.722| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 19567 Z= 0.447 Angle : 0.821 15.834 26603 Z= 0.435 Chirality : 0.055 0.275 3082 Planarity : 0.005 0.096 3426 Dihedral : 5.547 26.702 2872 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 5.38 % Allowed : 13.41 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.89 (0.16), residues: 2568 helix: 2.17 (0.27), residues: 401 sheet: -1.19 (0.17), residues: 881 loop : -0.98 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 94 TYR 0.040 0.003 TYR B 281 PHE 0.025 0.003 PHE D 64 TRP 0.028 0.003 TRP B 235 HIS 0.010 0.002 HIS F 95 Details of bonding type rmsd/Z covalent geometry : bond 0.01086 / 0.45 (19525) covalent geometry : angle 0.80636 / 0.43 (26513) SS BOND : bond 0.01014 / 0.68 ( 36) SS BOND : angle 3.01667 / 2.18 ( 72) hydrogen bonds : bond 0.04604 / 3.22 ( 695) hydrogen bonds : angle 5.84881 / 4.02 ( 2016) link_NAG-ASN : bond 0.00246 / 0.15 ( 6) link_NAG-ASN : angle 1.73714 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 293 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ASP cc_start: 0.8229 (t0) cc_final: 0.7893 (t0) REVERT: B 68 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 57 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8295 (ptp-170) REVERT: C 276 ILE cc_start: 0.8411 (mm) cc_final: 0.8205 (mt) REVERT: E 18 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: G 367 ASN cc_start: 0.7544 (p0) cc_final: 0.7161 (p0) REVERT: G 377 PRO cc_start: 0.8442 (Cg_exo) cc_final: 0.8179 (Cg_endo) REVERT: I 314 TRP cc_start: 0.7642 (m-90) cc_final: 0.7375 (m100) outliers start: 103 outliers final: 69 residues processed: 360 average time/residue: 0.1088 time to fit residues: 63.0989 Evaluate side-chains 351 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 279 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 17 LYS Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 372 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 290 CYS Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 107 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 37 optimal weight: 30.0000 chunk 184 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 239 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 103 ASN A 275 HIS B 237 ASN C 130 HIS C 275 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.198412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.177221 restraints weight = 19768.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.175976 restraints weight = 34812.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.174517 restraints weight = 33015.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.173035 restraints weight = 34330.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.171737 restraints weight = 35933.456| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 19567 Z= 0.131 Angle : 0.578 13.442 26603 Z= 0.306 Chirality : 0.045 0.229 3082 Planarity : 0.003 0.052 3426 Dihedral : 4.791 25.727 2870 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 3.03 % Allowed : 17.90 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.49 (0.17), residues: 2568 helix: 2.72 (0.27), residues: 401 sheet: -0.97 (0.18), residues: 860 loop : -0.79 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 24 TYR 0.015 0.001 TYR B 59 PHE 0.016 0.001 PHE E 64 TRP 0.012 0.001 TRP B 235 HIS 0.005 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (19525) covalent geometry : angle 0.56115 / 0.30 (26513) SS BOND : bond 0.00610 / 0.42 ( 36) SS BOND : angle 2.68064 / 1.87 ( 72) hydrogen bonds : bond 0.03093 / 2.18 ( 695) hydrogen bonds : angle 5.25492 / 3.60 ( 2016) link_NAG-ASN : bond 0.00251 / 0.13 ( 6) link_NAG-ASN : angle 1.34080 / 0.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8580 (m-80) cc_final: 0.8370 (m-80) REVERT: B 58 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (pt0) REVERT: B 67 ASP cc_start: 0.8100 (t0) cc_final: 0.7889 (t0) REVERT: C 276 ILE cc_start: 0.8370 (mm) cc_final: 0.8166 (mt) REVERT: G 367 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7170 (p0) outliers start: 58 outliers final: 41 residues processed: 299 average time/residue: 0.1043 time to fit residues: 50.5331 Evaluate side-chains 298 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 307 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 70 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 200 optimal weight: 20.0000 chunk 197 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN C 361 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.198769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.170104 restraints weight = 19800.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.169271 restraints weight = 34803.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.167784 restraints weight = 27969.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.164614 restraints weight = 31229.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.163146 restraints weight = 34076.942| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 19567 Z= 0.131 Angle : 0.548 12.251 26603 Z= 0.288 Chirality : 0.044 0.201 3082 Planarity : 0.003 0.042 3426 Dihedral : 4.532 25.211 2870 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 4.18 % Allowed : 17.48 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.33 (0.17), residues: 2568 helix: 2.91 (0.27), residues: 401 sheet: -0.87 (0.18), residues: 838 loop : -0.71 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 24 TYR 0.011 0.001 TYR C 139 PHE 0.017 0.001 PHE E 64 TRP 0.010 0.001 TRP B 235 HIS 0.005 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (19525) covalent geometry : angle 0.53404 / 0.28 (26513) SS BOND : bond 0.00630 / 0.43 ( 36) SS BOND : angle 2.39389 / 1.72 ( 72) hydrogen bonds : bond 0.02905 / 2.06 ( 695) hydrogen bonds : angle 5.00871 / 3.44 ( 2016) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 1.27895 / 0.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 262 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8580 (m-80) cc_final: 0.8359 (m-80) REVERT: B 67 ASP cc_start: 0.8352 (t0) cc_final: 0.8082 (t0) REVERT: C 328 MET cc_start: 0.7464 (ptp) cc_final: 0.7158 (ptp) REVERT: G 367 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7181 (p0) outliers start: 80 outliers final: 62 residues processed: 316 average time/residue: 0.0988 time to fit residues: 51.1732 Evaluate side-chains 318 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 41 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 307 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 255 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 140 optimal weight: 0.0670 chunk 21 optimal weight: 0.1980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.202913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.173319 restraints weight = 19640.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.171523 restraints weight = 31818.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.169677 restraints weight = 32885.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.168086 restraints weight = 32944.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.165308 restraints weight = 33244.480| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 19567 Z= 0.093 Angle : 0.505 11.305 26603 Z= 0.266 Chirality : 0.043 0.191 3082 Planarity : 0.003 0.040 3426 Dihedral : 4.125 22.781 2870 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 2.82 % Allowed : 19.15 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.07 (0.17), residues: 2568 helix: 3.15 (0.27), residues: 397 sheet: -0.63 (0.18), residues: 847 loop : -0.58 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 24 TYR 0.014 0.001 TYR C 139 PHE 0.018 0.001 PHE E 64 TRP 0.013 0.001 TRP B 314 HIS 0.003 0.000 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 (19525) covalent geometry : angle 0.49426 / 0.26 (26513) SS BOND : bond 0.00564 / 0.40 ( 36) SS BOND : angle 1.99098 / 1.42 ( 72) hydrogen bonds : bond 0.02568 / 1.83 ( 695) hydrogen bonds : angle 4.68129 / 3.23 ( 2016) link_NAG-ASN : bond 0.00270 / 0.14 ( 6) link_NAG-ASN : angle 1.14150 / 0.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ASP cc_start: 0.8036 (t0) cc_final: 0.7705 (t0) REVERT: G 367 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7084 (p0) outliers start: 54 outliers final: 39 residues processed: 301 average time/residue: 0.1027 time to fit residues: 50.1781 Evaluate side-chains 295 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 246 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 127 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 2.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN C 216 HIS E 27 ASN I 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.196230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.175515 restraints weight = 19774.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.173831 restraints weight = 35712.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.172419 restraints weight = 32673.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.171339 restraints weight = 31594.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.170410 restraints weight = 37711.832| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 19567 Z= 0.240 Angle : 0.621 12.797 26603 Z= 0.327 Chirality : 0.047 0.207 3082 Planarity : 0.004 0.050 3426 Dihedral : 4.666 26.596 2870 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 5.11 % Allowed : 18.22 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.31 (0.17), residues: 2568 helix: 2.95 (0.27), residues: 398 sheet: -0.91 (0.18), residues: 846 loop : -0.64 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 94 TYR 0.025 0.002 TYR C 132 PHE 0.026 0.002 PHE D 64 TRP 0.015 0.002 TRP B 235 HIS 0.008 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (19525) covalent geometry : angle 0.60441 / 0.32 (26513) SS BOND : bond 0.00741 / 0.49 ( 36) SS BOND : angle 2.73778 / 1.99 ( 72) hydrogen bonds : bond 0.03200 / 2.25 ( 695) hydrogen bonds : angle 4.89456 / 3.37 ( 2016) link_NAG-ASN : bond 0.00202 / 0.10 ( 6) link_NAG-ASN : angle 1.33372 / 0.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 266 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: -0.0062 (pmm) cc_final: -0.0311 (pmm) REVERT: B 202 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (pp) REVERT: C 248 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7784 (p90) REVERT: C 328 MET cc_start: 0.7511 (ptp) cc_final: 0.7209 (ptp) REVERT: G 282 HIS cc_start: 0.6828 (m-70) cc_final: 0.6614 (m-70) REVERT: G 284 LYS cc_start: 0.7614 (mmtt) cc_final: 0.6875 (mmtp) REVERT: G 367 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7134 (p0) outliers start: 98 outliers final: 77 residues processed: 334 average time/residue: 0.1050 time to fit residues: 56.8691 Evaluate side-chains 333 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 253 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 290 CYS Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 349 SER Chi-restraints excluded: chain I residue 382 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 145 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN E 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.199208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.169625 restraints weight = 19720.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.167043 restraints weight = 33539.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.165446 restraints weight = 33741.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.164309 restraints weight = 31975.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.162636 restraints weight = 31770.553| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 19567 Z= 0.134 Angle : 0.548 12.199 26603 Z= 0.288 Chirality : 0.044 0.199 3082 Planarity : 0.003 0.042 3426 Dihedral : 4.404 24.611 2870 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 3.76 % Allowed : 19.78 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.20 (0.17), residues: 2568 helix: 3.05 (0.27), residues: 398 sheet: -0.81 (0.18), residues: 831 loop : -0.61 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.016 0.001 TYR C 132 PHE 0.017 0.001 PHE E 64 TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 (19525) covalent geometry : angle 0.53359 / 0.28 (26513) SS BOND : bond 0.00637 / 0.44 ( 36) SS BOND : angle 2.40087 / 1.72 ( 72) hydrogen bonds : bond 0.02722 / 1.93 ( 695) hydrogen bonds : angle 4.73505 / 3.26 ( 2016) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 1.22512 / 0.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 262 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: -0.0125 (pmm) cc_final: -0.0358 (pmm) REVERT: B 202 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 277 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6717 (mt-10) REVERT: C 296 LYS cc_start: 0.7695 (ttmm) cc_final: 0.7286 (tttp) REVERT: C 328 MET cc_start: 0.7524 (ptp) cc_final: 0.7198 (ptp) REVERT: G 282 HIS cc_start: 0.6954 (m-70) cc_final: 0.6731 (m-70) REVERT: G 367 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7113 (p0) outliers start: 72 outliers final: 63 residues processed: 311 average time/residue: 0.1038 time to fit residues: 52.2337 Evaluate side-chains 321 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 155 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN E 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.196810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.176132 restraints weight = 19721.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.174916 restraints weight = 34520.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.172894 restraints weight = 31747.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.171742 restraints weight = 33402.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.170683 restraints weight = 35611.455| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 19567 Z= 0.211 Angle : 0.606 12.610 26603 Z= 0.317 Chirality : 0.046 0.205 3082 Planarity : 0.003 0.047 3426 Dihedral : 4.640 25.914 2870 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 4.49 % Allowed : 19.26 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.31 (0.17), residues: 2568 helix: 2.84 (0.27), residues: 404 sheet: -0.89 (0.18), residues: 830 loop : -0.65 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 94 TYR 0.018 0.002 TYR C 132 PHE 0.022 0.002 PHE D 64 TRP 0.014 0.001 TRP B 235 HIS 0.007 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (19525) covalent geometry : angle 0.58912 / 0.31 (26513) SS BOND : bond 0.00705 / 0.48 ( 36) SS BOND : angle 2.75716 / 2.00 ( 72) hydrogen bonds : bond 0.03030 / 2.14 ( 695) hydrogen bonds : angle 4.82782 / 3.32 ( 2016) link_NAG-ASN : bond 0.00215 / 0.11 ( 6) link_NAG-ASN : angle 1.31101 / 0.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: -0.0074 (pmm) cc_final: -0.0317 (pmm) REVERT: B 202 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8519 (pp) REVERT: B 257 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8665 (mp) REVERT: C 328 MET cc_start: 0.7513 (ptp) cc_final: 0.7209 (ptp) REVERT: G 284 LYS cc_start: 0.7604 (mmtt) cc_final: 0.6879 (mmtp) REVERT: G 367 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7132 (p0) REVERT: H 309 LYS cc_start: 0.7582 (pttp) cc_final: 0.6906 (pttm) outliers start: 86 outliers final: 74 residues processed: 320 average time/residue: 0.1127 time to fit residues: 58.1136 Evaluate side-chains 338 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 203 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 255 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN E 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.199928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.169875 restraints weight = 19761.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.167556 restraints weight = 33028.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.165350 restraints weight = 33074.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.163959 restraints weight = 34818.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.162955 restraints weight = 32042.835| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 19567 Z= 0.124 Angle : 0.546 11.841 26603 Z= 0.285 Chirality : 0.044 0.196 3082 Planarity : 0.003 0.041 3426 Dihedral : 4.356 24.332 2870 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 3.81 % Allowed : 19.83 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.17 (0.17), residues: 2568 helix: 3.08 (0.27), residues: 398 sheet: -0.79 (0.18), residues: 830 loop : -0.59 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 24 TYR 0.013 0.001 TYR C 132 PHE 0.017 0.001 PHE E 64 TRP 0.011 0.001 TRP H 314 HIS 0.003 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.12 (19525) covalent geometry : angle 0.53207 / 0.28 (26513) SS BOND : bond 0.00620 / 0.43 ( 36) SS BOND : angle 2.38183 / 1.72 ( 72) hydrogen bonds : bond 0.02647 / 1.89 ( 695) hydrogen bonds : angle 4.65455 / 3.21 ( 2016) link_NAG-ASN : bond 0.00246 / 0.12 ( 6) link_NAG-ASN : angle 1.17779 / 0.84 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 264 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: -0.0116 (pmm) cc_final: -0.0356 (pmm) REVERT: B 202 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (pp) REVERT: C 277 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6799 (mt-10) REVERT: C 328 MET cc_start: 0.7542 (ptp) cc_final: 0.7206 (ptp) REVERT: G 367 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7082 (p0) outliers start: 73 outliers final: 67 residues processed: 315 average time/residue: 0.1055 time to fit residues: 54.2614 Evaluate side-chains 326 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 290 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 367 ASN Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 186 CYS Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 333 SER Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 295 GLU Chi-restraints excluded: chain I residue 307 CYS Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 139 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 80 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 230 optimal weight: 0.1980 chunk 142 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.202073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.173067 restraints weight = 19739.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.171507 restraints weight = 31944.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.169863 restraints weight = 30440.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.168194 restraints weight = 32518.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.166361 restraints weight = 29793.110| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 19567 Z= 0.100 Angle : 0.521 11.543 26603 Z= 0.271 Chirality : 0.043 0.190 3082 Planarity : 0.003 0.040 3426 Dihedral : 4.126 23.269 2870 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 3.50 % Allowed : 20.30 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.01 (0.17), residues: 2568 helix: 3.21 (0.27), residues: 398 sheet: -0.63 (0.18), residues: 833 loop : -0.53 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 77 TYR 0.013 0.001 TYR C 132 PHE 0.017 0.001 PHE E 64 TRP 0.013 0.001 TRP H 314 HIS 0.003 0.000 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (19525) covalent geometry : angle 0.50817 / 0.27 (26513) SS BOND : bond 0.00580 / 0.41 ( 36) SS BOND : angle 2.17745 / 1.55 ( 72) hydrogen bonds : bond 0.02505 / 1.80 ( 695) hydrogen bonds : angle 4.48866 / 3.10 ( 2016) link_NAG-ASN : bond 0.00259 / 0.13 ( 6) link_NAG-ASN : angle 1.10621 / 0.80 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.45 seconds wall clock time: 49 minutes 45.84 seconds (2985.84 seconds total)