Starting phenix.real_space_refine on Fri Feb 23 02:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3l_31683/02_2024/7v3l_31683_neut.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 195 5.16 5 C 22952 2.51 5 N 6002 2.21 5 O 7089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 793": "OE1" <-> "OE2" Residue "B ASP 868": "OD1" <-> "OD2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1179": "NH1" <-> "NH2" Residue "B ASP 1182": "OD1" <-> "OD2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 644": "OD1" <-> "OD2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ASP 726": "OD1" <-> "OD2" Residue "C ASP 868": "OD1" <-> "OD2" Residue "C GLU 875": "OE1" <-> "OE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C GLU 992": "OE1" <-> "OE2" Residue "C PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "E ARG 6": "NH1" <-> "NH2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "G ARG 6": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 215": "NH1" <-> "NH2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 228": "NH1" <-> "NH2" Residue "I ARG 6": "NH1" <-> "NH2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 215": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36238 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1131, 8731 Classifications: {'peptide': 1131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1080} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 1131, 8731 Classifications: {'peptide': 1131} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 1080} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8785 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 8779 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1084} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 1135, 8779 Classifications: {'peptide': 1135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1084} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 8968 Chain: "C" Number of atoms: 8719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1126, 8713 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 49, 'TRANS': 1076} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 1126, 8713 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 49, 'TRANS': 1076} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 8899 Chain: "D" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1688 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1688 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1681 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1638 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 32.48, per 1000 atoms: 0.90 Number of scatterers: 36238 At special positions: 0 Unit cell: (199.801, 234.176, 226.656, 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 195 16.00 O 7089 8.00 N 6002 7.00 C 22952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.05 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.02 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.05 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.05 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.06 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.02 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.05 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.05 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.06 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 91 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 198 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS H 158 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 11.6 seconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8766 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 85 sheets defined 19.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.020A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.535A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.847A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.948A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.554A pdb=" N GLN A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.594A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.526A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.615A pdb=" N ASN A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1013 through 1016 Processing helix chain 'A' and resid 1017 through 1043 removed outlier: 4.241A pdb=" N THR A1043 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1106 Processing helix chain 'A' and resid 1114 through 1118 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.747A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.328A pdb=" N SER B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.857A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.668A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 529 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 825 through 852 removed outlier: 3.715A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.739A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.530A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN B 994 " --> pdb=" O LEU B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1011 removed outlier: 3.505A pdb=" N GLY B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1041 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.825A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B1073 " --> pdb=" O ARG B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1177 removed outlier: 3.990A pdb=" N ASN B1176 " --> pdb=" O ILE B1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.945A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.733A pdb=" N GLN C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.957A pdb=" N SER C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 825 through 852 removed outlier: 3.780A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.789A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.906A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 987 through 993 Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1016 through 1035 removed outlier: 3.541A pdb=" N GLN C1020 " --> pdb=" O ASN C1016 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 4.238A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 203 through 210 removed outlier: 3.560A pdb=" N GLY D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 203 through 210 removed outlier: 3.560A pdb=" N GLY F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 203 through 210 Processing helix chain 'I' and resid 125 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.696A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.431A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.089A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.741A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.741A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 182 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.207A pdb=" N HIS A 208 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 366 removed outlier: 4.671A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 662 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 671 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 569 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 482 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 477 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU A 554 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL A 514 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 605 through 607 removed outlier: 3.618A pdb=" N TYR A 606 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AB7, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.656A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 967 through 968 removed outlier: 3.989A pdb=" N PHE A 967 " --> pdb=" O SER C 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1122 through 1124 removed outlier: 3.888A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1127 through 1130 Processing sheet with id=AC2, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.435A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.589A pdb=" N GLU B 252 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.555A pdb=" N ILE B 300 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.730A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 293 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 148 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.730A pdb=" N LYS B 110 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 293 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 148 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 182 " --> pdb=" O TYR B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.723A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AD2, first strand: chain 'B' and resid 360 through 367 removed outlier: 5.365A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 569 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 482 " --> pdb=" O MET B 569 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 477 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU B 554 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL B 514 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 606 through 607 removed outlier: 3.595A pdb=" N GLY B 613 " --> pdb=" O TYR B 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 617 through 619 Processing sheet with id=AD8, first strand: chain 'B' and resid 778 through 783 removed outlier: 3.649A pdb=" N PHE B 778 " --> pdb=" O SER B1151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 793 through 794 removed outlier: 3.514A pdb=" N PHE B1126 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE2, first strand: chain 'B' and resid 1155 through 1156 Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.855A pdb=" N VAL C 102 " --> pdb=" O ASP C 34 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.402A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.532A pdb=" N TYR C 292 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 150 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 235 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.606A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 120 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.684A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE9, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AF1, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AF2, first strand: chain 'C' and resid 400 through 405 removed outlier: 3.700A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 477 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 422 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 498 through 499 removed outlier: 4.384A pdb=" N LEU C 554 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 504 through 506 removed outlier: 3.831A pdb=" N VAL C 514 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 605 through 607 Processing sheet with id=AF6, first strand: chain 'C' and resid 1122 through 1124 Processing sheet with id=AF7, first strand: chain 'C' and resid 1127 through 1130 Processing sheet with id=AF8, first strand: chain 'D' and resid 6 through 9 Processing sheet with id=AF9, first strand: chain 'D' and resid 14 through 15 removed outlier: 4.081A pdb=" N GLY D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 138 through 141 removed outlier: 4.694A pdb=" N ASP D 162 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR D 194 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.528A pdb=" N HIS D 218 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 223 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AG4, first strand: chain 'E' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU E 14 " --> pdb=" O GLU E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AG6, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.628A pdb=" N GLN E 93 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR E 101 " --> pdb=" O GLN E 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AG8, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.752A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP E 152 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 200 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL E 209 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 6 through 9 Processing sheet with id=AH2, first strand: chain 'F' and resid 14 through 15 removed outlier: 4.081A pdb=" N GLY F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 138 through 141 removed outlier: 4.694A pdb=" N ASP F 162 " --> pdb=" O TYR F 194 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR F 194 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.528A pdb=" N HIS F 218 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 223 " --> pdb=" O HIS F 218 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 7 through 8 Processing sheet with id=AH6, first strand: chain 'G' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU G 14 " --> pdb=" O GLU G 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AH8, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.628A pdb=" N GLN G 93 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR G 101 " --> pdb=" O GLN G 93 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AI1, first strand: chain 'G' and resid 118 through 122 removed outlier: 5.752A pdb=" N TYR G 177 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP G 152 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS G 149 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL G 200 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL G 209 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AI4, first strand: chain 'H' and resid 14 through 15 removed outlier: 4.082A pdb=" N GLY H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 138 through 141 removed outlier: 3.670A pdb=" N LEU H 196 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 169 through 172 removed outlier: 3.714A pdb=" N HIS H 218 " --> pdb=" O THR H 223 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 223 " --> pdb=" O HIS H 218 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AI8, first strand: chain 'I' and resid 14 through 15 removed outlier: 6.386A pdb=" N LEU I 14 " --> pdb=" O GLU I 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'I' and resid 22 through 24 Processing sheet with id=AJ1, first strand: chain 'I' and resid 47 through 49 Processing sheet with id=AJ2, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AJ3, first strand: chain 'I' and resid 118 through 122 removed outlier: 5.751A pdb=" N TYR I 177 " --> pdb=" O ASN I 142 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'I' and resid 157 through 159 removed outlier: 4.682A pdb=" N TRP I 152 " --> pdb=" O GLN I 159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS I 149 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 200 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL I 209 " --> pdb=" O VAL I 200 " (cutoff:3.500A) 1233 hydrogen bonds defined for protein. 3258 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: 17.15 Time building geometry restraints manager: 15.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5964 1.31 - 1.44: 10400 1.44 - 1.57: 20435 1.57 - 1.70: 0 1.70 - 1.83: 255 Bond restraints: 37054 Sorted by residual: bond pdb=" C ARG D 111 " pdb=" N TYR D 112 " ideal model delta sigma weight residual 1.332 1.475 -0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" C PRO A 449 " pdb=" N LEU A 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.28e+01 bond pdb=" C PRO B 449 " pdb=" N LEU B 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.26e+01 bond pdb=" C PRO C 449 " pdb=" N LEU C 450 " ideal model delta sigma weight residual 1.335 1.441 -0.106 1.34e-02 5.57e+03 6.26e+01 bond pdb=" C VAL C 575 " pdb=" N GLN C 576 " ideal model delta sigma weight residual 1.330 1.428 -0.098 1.32e-02 5.74e+03 5.52e+01 ... (remaining 37049 not shown) Histogram of bond angle deviations from ideal: 97.59 - 104.99: 812 104.99 - 112.39: 17268 112.39 - 119.79: 16453 119.79 - 127.19: 15589 127.19 - 134.59: 256 Bond angle restraints: 50378 Sorted by residual: angle pdb=" N VAL B 714 " pdb=" CA VAL B 714 " pdb=" C VAL B 714 " ideal model delta sigma weight residual 112.12 102.71 9.41 8.40e-01 1.42e+00 1.26e+02 angle pdb=" N ILE A 997 " pdb=" CA ILE A 997 " pdb=" C ILE A 997 " ideal model delta sigma weight residual 113.00 99.89 13.11 1.30e+00 5.92e-01 1.02e+02 angle pdb=" N SER A 695 " pdb=" CA SER A 695 " pdb=" C SER A 695 " ideal model delta sigma weight residual 113.97 102.18 11.79 1.28e+00 6.10e-01 8.49e+01 angle pdb=" N PRO F 165 " pdb=" CA PRO F 165 " pdb=" C PRO F 165 " ideal model delta sigma weight residual 113.53 125.48 -11.95 1.39e+00 5.18e-01 7.39e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 112.93 103.33 9.60 1.12e+00 7.97e-01 7.35e+01 ... (remaining 50373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 19965 18.04 - 36.09: 1539 36.09 - 54.13: 431 54.13 - 72.17: 118 72.17 - 90.22: 18 Dihedral angle restraints: 22071 sinusoidal: 8368 harmonic: 13703 Sorted by residual: dihedral pdb=" CB CYS B1106 " pdb=" SG CYS B1106 " pdb=" SG CYS B1117 " pdb=" CB CYS B1117 " ideal model delta sinusoidal sigma weight residual 93.00 -176.78 -90.22 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS C1106 " pdb=" SG CYS C1106 " pdb=" SG CYS C1117 " pdb=" CB CYS C1117 " ideal model delta sinusoidal sigma weight residual 93.00 170.12 -77.12 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" C TYR C 642 " pdb=" N TYR C 642 " pdb=" CA TYR C 642 " pdb=" CB TYR C 642 " ideal model delta harmonic sigma weight residual -122.60 -143.14 20.54 0 2.50e+00 1.60e-01 6.75e+01 ... (remaining 22068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4929 0.150 - 0.300: 688 0.300 - 0.450: 54 0.450 - 0.600: 1 0.600 - 0.751: 3 Chirality restraints: 5675 Sorted by residual: chirality pdb=" CA TYR C 642 " pdb=" N TYR C 642 " pdb=" C TYR C 642 " pdb=" CB TYR C 642 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA TYR C 641 " pdb=" N TYR C 641 " pdb=" C TYR C 641 " pdb=" CB TYR C 641 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA THR B1077 " pdb=" N THR B1077 " pdb=" C THR B1077 " pdb=" CB THR B1077 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 5672 not shown) Planarity restraints: 6483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASER A 51 " 0.030 2.00e-02 2.50e+03 6.27e-02 3.94e+01 pdb=" C ASER A 51 " -0.108 2.00e-02 2.50e+03 pdb=" O ASER A 51 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS A 52 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BSER A 51 " 0.030 2.00e-02 2.50e+03 6.16e-02 3.79e+01 pdb=" C BSER A 51 " -0.107 2.00e-02 2.50e+03 pdb=" O BSER A 51 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS A 52 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 323 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PHE C 323 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE C 323 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU C 324 " -0.023 2.00e-02 2.50e+03 ... (remaining 6480 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 549 2.64 - 3.21: 33309 3.21 - 3.77: 56183 3.77 - 4.34: 78345 4.34 - 4.90: 122663 Nonbonded interactions: 291049 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OD2 ASP A 288 " model vdw 2.080 2.440 nonbonded pdb=" OH TYR C 58 " pdb=" O GLY C 331 " model vdw 2.100 2.440 nonbonded pdb=" OH TYR B 58 " pdb=" O GLY B 331 " model vdw 2.110 2.440 nonbonded pdb=" O THR C 212 " pdb=" OG SER C 215 " model vdw 2.113 2.440 nonbonded pdb=" O SER A 88 " pdb=" OG SER A 299 " model vdw 2.167 2.440 ... (remaining 291044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 60 or resid 63 through 4 \ 21 or (resid 422 and (name N or name CA or name C or name O or name CB )) or res \ id 423 through 480 or (resid 481 through 482 and (name N or name CA or name C or \ name O or name CB )) or resid 483 through 641 or (resid 642 and (name N or name \ CA or name C or name O or name CB )) or resid 643 through 676 or resid 678 thro \ ugh 1043 or resid 1045 through 1164 or resid 1171 through 1178 or resid 1182 thr \ ough 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 86 or resid 88 through 4 \ 21 or (resid 422 and (name N or name CA or name C or name O or name CB )) or res \ id 423 through 480 or (resid 481 through 482 and (name N or name CA or name C or \ name O or name CB )) or resid 483 through 586 or resid 596 through 676 or resid \ 678 through 690 or resid 692 through 723 or (resid 724 through 725 and (name N \ or name CA or name C or name O or name CB )) or resid 726 through 743 or resid 7 \ 57 or (resid 758 through 760 and (name N or name CA or name C or name O or name \ CB )) or resid 761 through 1164 or resid 1171 through 1173 or resid 1175 through \ 1178 or resid 1182 through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 60 or resid 63 through 5 \ 86 or resid 596 through 641 or (resid 642 and (name N or name CA or name C or na \ me O or name CB )) or resid 643 through 690 or resid 692 through 723 or (resid 7 \ 24 through 725 and (name N or name CA or name C or name O or name CB )) or resid \ 726 through 743 or resid 757 or (resid 758 through 760 and (name N or name CA o \ r name C or name O or name CB )) or resid 761 through 1043 or resid 1045 through \ 1206)) } ncs_group { reference = (chain 'D' and (resid 4 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 229)) selection = (chain 'F' and (resid 4 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 229)) selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 4 through 215) selection = (chain 'G' and resid 4 through 215) 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.040 Extract box with map and model: 9.150 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 119.450 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 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 : 0.012 0.143 37054 Z= 0.820 Angle : 1.549 17.526 50378 Z= 1.103 Chirality : 0.103 0.751 5675 Planarity : 0.006 0.084 6483 Dihedral : 14.532 89.898 13161 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.21 % Favored : 87.91 % Rotamer: Outliers : 7.18 % Allowed : 8.34 % Favored : 84.48 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4641 helix: 0.62 (0.19), residues: 725 sheet: 0.40 (0.16), residues: 1168 loop : -1.94 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 310 HIS 0.010 0.002 HIS C 298 PHE 0.046 0.003 PHE C1136 TYR 0.046 0.003 TYR C 77 ARG 0.012 0.001 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 516 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.6847 (mp) cc_final: 0.6626 (mt) REVERT: A 240 MET cc_start: 0.6732 (pmm) cc_final: 0.6331 (pmm) REVERT: A 484 VAL cc_start: 0.1675 (OUTLIER) cc_final: 0.1329 (p) REVERT: A 629 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6692 (mmt90) REVERT: A 940 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7836 (p0) REVERT: B 101 PHE cc_start: 0.6716 (m-10) cc_final: 0.6511 (m-80) REVERT: B 161 MET cc_start: 0.5920 (mmp) cc_final: 0.5635 (mmt) REVERT: B 218 ASN cc_start: 0.7291 (t0) cc_final: 0.7090 (t0) REVERT: B 240 MET cc_start: 0.7658 (tpp) cc_final: 0.7235 (tpp) REVERT: B 433 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3913 (mm) REVERT: B 483 THR cc_start: 0.3914 (OUTLIER) cc_final: 0.3689 (p) REVERT: B 1008 MET cc_start: 0.7842 (ttp) cc_final: 0.7380 (ttp) REVERT: B 1056 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6198 (mp10) REVERT: B 1173 ILE cc_start: 0.5430 (tp) cc_final: 0.5128 (pt) REVERT: C 183 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6453 (p90) REVERT: C 208 HIS cc_start: 0.6087 (p90) cc_final: 0.5710 (p-80) REVERT: C 486 HIS cc_start: 0.3960 (OUTLIER) cc_final: 0.2468 (t70) REVERT: C 960 TRP cc_start: 0.6519 (OUTLIER) cc_final: 0.5162 (t60) REVERT: C 1043 THR cc_start: 0.5498 (OUTLIER) cc_final: 0.5107 (p) REVERT: D 48 LEU cc_start: -0.0695 (OUTLIER) cc_final: -0.1058 (tt) REVERT: F 23 VAL cc_start: 0.3733 (OUTLIER) cc_final: 0.3481 (m) REVERT: F 51 MET cc_start: 0.3161 (OUTLIER) cc_final: 0.1408 (ppp) REVERT: F 84 MET cc_start: 0.1668 (tmm) cc_final: 0.1032 (tmm) REVERT: F 103 TYR cc_start: 0.2741 (t80) cc_final: 0.2115 (t80) REVERT: F 112 TYR cc_start: 0.4764 (OUTLIER) cc_final: 0.4164 (t80) REVERT: F 170 VAL cc_start: 0.0451 (OUTLIER) cc_final: 0.0028 (t) REVERT: F 200 VAL cc_start: 0.4761 (m) cc_final: 0.4384 (p) REVERT: G 97 TYR cc_start: 0.1019 (OUTLIER) cc_final: -0.0376 (p90) REVERT: G 150 VAL cc_start: 0.0703 (OUTLIER) cc_final: 0.0132 (m) REVERT: G 153 LYS cc_start: 0.0616 (OUTLIER) cc_final: -0.0375 (mmmt) REVERT: G 213 PHE cc_start: -0.0447 (OUTLIER) cc_final: -0.2038 (m-10) REVERT: H 202 VAL cc_start: 0.1461 (OUTLIER) cc_final: 0.1246 (p) REVERT: I 97 TYR cc_start: 0.1451 (OUTLIER) cc_final: -0.0316 (p90) REVERT: I 153 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.0711 (mmmt) REVERT: I 213 PHE cc_start: -0.1075 (OUTLIER) cc_final: -0.2051 (t80) outliers start: 291 outliers final: 55 residues processed: 745 average time/residue: 0.4555 time to fit residues: 560.3817 Evaluate side-chains 346 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 268 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 430 PRO Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1056 GLN Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1048 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 112 TYR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 213 PHE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 LYS Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 238 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 272 optimal weight: 30.0000 chunk 424 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 599 GLN A 812 ASN A 993 ASN A 999 ASN A1056 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 ASN A1176 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 167 HIS B 346 GLN B 408 ASN B1016 ASN B1072 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN B1163 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN C 647 ASN C 719 ASN C 785 ASN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN C1146 HIS C1163 ASN D 6 GLN D 108 ASN D 114 GLN D 189 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 93 GLN E 96 ASN E 128 GLN E 142 ASN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN G 142 ASN G 164 GLN H 210 GLN I 93 GLN I 96 ASN I 142 ASN I 164 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37054 Z= 0.278 Angle : 0.803 12.728 50378 Z= 0.424 Chirality : 0.048 0.293 5675 Planarity : 0.005 0.064 6483 Dihedral : 7.762 58.680 5207 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.72 % Favored : 90.65 % Rotamer: Outliers : 3.65 % Allowed : 12.98 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 4641 helix: 0.75 (0.19), residues: 762 sheet: 0.35 (0.16), residues: 1196 loop : -1.94 (0.11), residues: 2683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 35 HIS 0.008 0.002 HIS C1122 PHE 0.030 0.002 PHE A 723 TYR 0.030 0.002 TYR B 241 ARG 0.014 0.001 ARG C1113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 304 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 PRO cc_start: 0.3259 (Cg_exo) cc_final: 0.3049 (Cg_endo) REVERT: A 486 HIS cc_start: 0.4376 (OUTLIER) cc_final: 0.4164 (p-80) REVERT: A 629 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6872 (mmm-85) REVERT: A 960 TRP cc_start: 0.4951 (t-100) cc_final: 0.1235 (t-100) REVERT: B 101 PHE cc_start: 0.6963 (m-10) cc_final: 0.6332 (m-80) REVERT: B 161 MET cc_start: 0.5918 (mmp) cc_final: 0.5703 (mmt) REVERT: B 376 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6814 (mp0) REVERT: B 842 GLN cc_start: 0.7884 (tp40) cc_final: 0.7609 (tp40) REVERT: B 987 GLN cc_start: 0.6375 (tt0) cc_final: 0.4916 (tt0) REVERT: B 1173 ILE cc_start: 0.5674 (tp) cc_final: 0.5244 (pt) REVERT: B 1192 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.3736 (m-80) REVERT: C 183 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6575 (p90) REVERT: C 204 PHE cc_start: 0.5421 (p90) cc_final: 0.5206 (p90) REVERT: C 865 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: C 960 TRP cc_start: 0.6724 (OUTLIER) cc_final: 0.5030 (t60) REVERT: C 1008 MET cc_start: 0.7621 (ttm) cc_final: 0.7264 (tpp) REVERT: C 1043 THR cc_start: 0.6024 (OUTLIER) cc_final: 0.5634 (p) REVERT: C 1201 ASN cc_start: 0.7133 (t0) cc_final: 0.6753 (t0) REVERT: D 51 MET cc_start: -0.0587 (ptt) cc_final: -0.0816 (ptt) REVERT: D 84 MET cc_start: 0.0242 (tmm) cc_final: -0.0018 (ttp) REVERT: E 92 GLN cc_start: 0.0448 (OUTLIER) cc_final: 0.0147 (tp40) REVERT: F 51 MET cc_start: 0.2721 (OUTLIER) cc_final: 0.1034 (ppp) REVERT: F 103 TYR cc_start: 0.2896 (t80) cc_final: 0.2203 (t80) REVERT: F 200 VAL cc_start: 0.4868 (m) cc_final: 0.4229 (p) REVERT: G 97 TYR cc_start: 0.1082 (OUTLIER) cc_final: -0.0362 (p90) REVERT: G 110 ILE cc_start: 0.2071 (OUTLIER) cc_final: 0.1518 (pt) REVERT: G 153 LYS cc_start: 0.0956 (OUTLIER) cc_final: -0.0249 (mmmm) REVERT: G 203 GLN cc_start: 0.1405 (mp10) cc_final: 0.1187 (tt0) REVERT: I 94 TYR cc_start: 0.0267 (p90) cc_final: -0.0197 (p90) REVERT: I 97 TYR cc_start: 0.1027 (OUTLIER) cc_final: -0.0810 (p90) REVERT: I 187 LYS cc_start: 0.2033 (OUTLIER) cc_final: 0.1564 (tptp) outliers start: 148 outliers final: 69 residues processed: 430 average time/residue: 0.4579 time to fit residues: 332.1646 Evaluate side-chains 330 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 4.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1057 ARG Chi-restraints excluded: chain B residue 1192 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 352 optimal weight: 0.0570 chunk 288 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 chunk 458 optimal weight: 0.0670 chunk 378 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 chunk 340 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 319 GLN ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 114 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN I 159 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37054 Z= 0.184 Angle : 0.693 11.127 50378 Z= 0.363 Chirality : 0.046 0.266 5675 Planarity : 0.004 0.053 6483 Dihedral : 6.535 59.638 5135 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.00 % Favored : 90.52 % Rotamer: Outliers : 2.79 % Allowed : 14.51 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 4641 helix: 1.08 (0.19), residues: 756 sheet: 0.44 (0.16), residues: 1168 loop : -1.88 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 35 HIS 0.005 0.001 HIS B 298 PHE 0.027 0.002 PHE A 778 TYR 0.035 0.002 TYR C 641 ARG 0.005 0.000 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 266 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.6983 (mtp) cc_final: 0.6714 (mtp) REVERT: A 452 MET cc_start: 0.2347 (ptp) cc_final: 0.2119 (ptt) REVERT: A 455 ASP cc_start: 0.2213 (t0) cc_final: 0.1062 (m-30) REVERT: A 485 PRO cc_start: 0.3396 (Cg_exo) cc_final: 0.3158 (Cg_endo) REVERT: A 486 HIS cc_start: 0.4378 (OUTLIER) cc_final: 0.4134 (p-80) REVERT: A 608 LEU cc_start: 0.5259 (mt) cc_final: 0.4738 (mt) REVERT: A 629 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7215 (mmm-85) REVERT: A 960 TRP cc_start: 0.4961 (t-100) cc_final: 0.1617 (t-100) REVERT: B 161 MET cc_start: 0.6163 (mmp) cc_final: 0.5687 (mmt) REVERT: B 842 GLN cc_start: 0.7903 (tp40) cc_final: 0.7583 (tp40) REVERT: B 1173 ILE cc_start: 0.5717 (tp) cc_final: 0.5307 (pt) REVERT: C 183 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6439 (p90) REVERT: C 563 MET cc_start: 0.1467 (mtp) cc_final: 0.0204 (ptp) REVERT: C 582 ASN cc_start: 0.2941 (t0) cc_final: 0.2494 (t0) REVERT: C 960 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.5052 (t60) REVERT: C 1008 MET cc_start: 0.7445 (ttm) cc_final: 0.6963 (tpp) REVERT: C 1043 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5783 (p) REVERT: D 60 THR cc_start: 0.1011 (OUTLIER) cc_final: 0.0556 (t) REVERT: D 120 TRP cc_start: 0.1901 (m100) cc_final: 0.1397 (m100) REVERT: E 213 PHE cc_start: -0.1582 (OUTLIER) cc_final: -0.2473 (m-80) REVERT: F 51 MET cc_start: 0.2861 (OUTLIER) cc_final: 0.1378 (ppp) REVERT: F 84 MET cc_start: 0.1306 (tmm) cc_final: 0.0948 (tmm) REVERT: F 103 TYR cc_start: 0.2936 (t80) cc_final: 0.2162 (t80) REVERT: G 97 TYR cc_start: 0.0843 (OUTLIER) cc_final: -0.0546 (p90) REVERT: G 110 ILE cc_start: 0.1698 (OUTLIER) cc_final: 0.1283 (pt) REVERT: G 153 LYS cc_start: 0.0974 (OUTLIER) cc_final: -0.0349 (mmmm) REVERT: G 203 GLN cc_start: 0.1214 (mp10) cc_final: 0.1006 (tt0) REVERT: I 97 TYR cc_start: 0.0978 (OUTLIER) cc_final: -0.0844 (p90) REVERT: I 187 LYS cc_start: 0.2017 (mmtm) cc_final: 0.1519 (tptp) outliers start: 113 outliers final: 68 residues processed: 358 average time/residue: 0.4623 time to fit residues: 283.0383 Evaluate side-chains 321 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 241 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1179 ARG Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 202 optimal weight: 0.0970 chunk 285 optimal weight: 0.9980 chunk 426 optimal weight: 6.9990 chunk 451 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 404 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1031 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 114 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37054 Z= 0.185 Angle : 0.667 11.980 50378 Z= 0.348 Chirality : 0.045 0.292 5675 Planarity : 0.004 0.050 6483 Dihedral : 6.230 58.355 5126 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.22 % Favored : 90.35 % Rotamer: Outliers : 2.99 % Allowed : 14.93 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4641 helix: 1.28 (0.20), residues: 738 sheet: 0.40 (0.16), residues: 1178 loop : -1.85 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 35 HIS 0.004 0.001 HIS B1138 PHE 0.034 0.002 PHE A 778 TYR 0.035 0.002 TYR C 641 ARG 0.013 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 260 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.2236 (ptp) cc_final: 0.1850 (ptt) REVERT: A 455 ASP cc_start: 0.1987 (t0) cc_final: 0.1188 (m-30) REVERT: A 629 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7246 (tpp80) REVERT: A 960 TRP cc_start: 0.5012 (t-100) cc_final: 0.2406 (t-100) REVERT: B 161 MET cc_start: 0.6259 (mmp) cc_final: 0.5870 (mmt) REVERT: B 621 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6926 (p) REVERT: B 842 GLN cc_start: 0.7853 (tp40) cc_final: 0.7579 (tp40) REVERT: B 1173 ILE cc_start: 0.5845 (tp) cc_final: 0.5407 (pt) REVERT: C 183 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6589 (p90) REVERT: C 582 ASN cc_start: 0.3215 (m-40) cc_final: 0.2785 (t0) REVERT: C 960 TRP cc_start: 0.6694 (OUTLIER) cc_final: 0.5349 (t60) REVERT: C 1008 MET cc_start: 0.7441 (ttm) cc_final: 0.7107 (tpp) REVERT: C 1012 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7236 (t80) REVERT: C 1043 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6138 (p) REVERT: F 51 MET cc_start: 0.2183 (OUTLIER) cc_final: 0.0921 (ppp) REVERT: F 170 VAL cc_start: 0.0892 (OUTLIER) cc_final: 0.0611 (t) REVERT: G 97 TYR cc_start: 0.0573 (OUTLIER) cc_final: -0.0724 (p90) REVERT: G 110 ILE cc_start: 0.1891 (OUTLIER) cc_final: 0.1445 (pt) REVERT: I 97 TYR cc_start: 0.0745 (OUTLIER) cc_final: -0.1023 (p90) outliers start: 121 outliers final: 78 residues processed: 356 average time/residue: 0.4420 time to fit residues: 269.1391 Evaluate side-chains 323 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 234 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1057 ARG Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 385 optimal weight: 20.0000 chunk 312 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 405 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1169 ASN A1201 ASN B 114 ASN B 516 GLN B 688 GLN B 785 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 ASN B1145 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN C1163 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 37054 Z= 0.397 Angle : 0.842 13.652 50378 Z= 0.446 Chirality : 0.052 0.387 5675 Planarity : 0.006 0.093 6483 Dihedral : 7.068 58.931 5117 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.27 % Favored : 88.32 % Rotamer: Outliers : 3.78 % Allowed : 14.98 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4641 helix: 0.51 (0.19), residues: 748 sheet: -0.04 (0.15), residues: 1221 loop : -2.02 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 35 HIS 0.009 0.002 HIS B1138 PHE 0.032 0.003 PHE A 778 TYR 0.048 0.003 TYR B 641 ARG 0.007 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 267 time to evaluate : 4.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.5046 (mttt) cc_final: 0.4844 (tptm) REVERT: A 148 MET cc_start: 0.6806 (mtp) cc_final: 0.6555 (ptp) REVERT: A 231 TYR cc_start: 0.6770 (m-10) cc_final: 0.6440 (m-80) REVERT: A 452 MET cc_start: 0.2234 (ptp) cc_final: 0.1165 (ptp) REVERT: A 455 ASP cc_start: 0.2233 (t0) cc_final: 0.1630 (m-30) REVERT: A 486 HIS cc_start: 0.4759 (OUTLIER) cc_final: 0.4281 (p-80) REVERT: A 960 TRP cc_start: 0.5127 (t-100) cc_final: 0.2777 (t-100) REVERT: B 161 MET cc_start: 0.6095 (mmp) cc_final: 0.5737 (mmt) REVERT: B 232 PHE cc_start: 0.7296 (m-80) cc_final: 0.6992 (t80) REVERT: B 240 MET cc_start: 0.7187 (tpp) cc_final: 0.6952 (tpp) REVERT: B 367 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: B 1060 VAL cc_start: 0.6019 (m) cc_final: 0.5759 (p) REVERT: B 1173 ILE cc_start: 0.5885 (tp) cc_final: 0.5390 (pt) REVERT: C 183 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6444 (p90) REVERT: C 960 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.5537 (t60) REVERT: D 60 THR cc_start: 0.0688 (OUTLIER) cc_final: 0.0362 (t) REVERT: E 213 PHE cc_start: -0.0995 (OUTLIER) cc_final: -0.2336 (m-80) REVERT: F 51 MET cc_start: 0.1743 (OUTLIER) cc_final: 0.0811 (ppp) REVERT: G 7 MET cc_start: 0.2921 (OUTLIER) cc_final: 0.2671 (ttt) REVERT: G 97 TYR cc_start: 0.0813 (OUTLIER) cc_final: -0.0067 (p90) REVERT: G 110 ILE cc_start: 0.1840 (OUTLIER) cc_final: 0.1506 (pt) REVERT: I 97 TYR cc_start: 0.0884 (OUTLIER) cc_final: -0.1072 (p90) outliers start: 153 outliers final: 98 residues processed: 392 average time/residue: 0.4391 time to fit residues: 294.6487 Evaluate side-chains 337 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 228 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 928 TYR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1191 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1162 THR Chi-restraints excluded: chain C residue 1191 PHE Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 1.9990 chunk 406 optimal weight: 20.0000 chunk 89 optimal weight: 0.0670 chunk 265 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 451 optimal weight: 0.0970 chunk 375 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN A1169 ASN A1177 ASN B 815 GLN B 842 GLN B 987 GLN B1031 GLN B1145 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN C1177 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37054 Z= 0.170 Angle : 0.672 14.582 50378 Z= 0.349 Chirality : 0.045 0.340 5675 Planarity : 0.004 0.058 6483 Dihedral : 6.135 58.739 5113 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.09 % Favored : 90.57 % Rotamer: Outliers : 2.71 % Allowed : 16.14 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4641 helix: 1.15 (0.20), residues: 731 sheet: 0.22 (0.16), residues: 1176 loop : -1.90 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 35 HIS 0.007 0.001 HIS B1146 PHE 0.036 0.001 PHE A 778 TYR 0.034 0.001 TYR C 641 ARG 0.008 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 253 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6380 (m-10) cc_final: 0.6093 (m-80) REVERT: A 452 MET cc_start: 0.2253 (ptp) cc_final: 0.1638 (ptt) REVERT: A 455 ASP cc_start: 0.2099 (t0) cc_final: 0.1197 (m-30) REVERT: A 486 HIS cc_start: 0.4711 (OUTLIER) cc_final: 0.4263 (p-80) REVERT: A 629 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7379 (tpp80) REVERT: A 960 TRP cc_start: 0.5157 (t-100) cc_final: 0.1831 (t-100) REVERT: A 988 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: A 1112 LYS cc_start: 0.7552 (tppt) cc_final: 0.7241 (mmmt) REVERT: B 161 MET cc_start: 0.6261 (mmp) cc_final: 0.5889 (mmt) REVERT: B 232 PHE cc_start: 0.7175 (m-80) cc_final: 0.6757 (t80) REVERT: B 1060 VAL cc_start: 0.5912 (m) cc_final: 0.5691 (p) REVERT: B 1173 ILE cc_start: 0.5548 (tp) cc_final: 0.5263 (pt) REVERT: C 183 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6432 (p90) REVERT: C 563 MET cc_start: 0.3020 (mtt) cc_final: 0.0547 (ptp) REVERT: C 569 MET cc_start: 0.0469 (mtm) cc_final: -0.0963 (mmp) REVERT: C 960 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.5412 (t60) REVERT: C 1012 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7618 (t80) REVERT: C 1053 ASP cc_start: 0.7342 (m-30) cc_final: 0.6968 (p0) REVERT: D 60 THR cc_start: 0.0747 (OUTLIER) cc_final: 0.0280 (t) REVERT: D 120 TRP cc_start: 0.1820 (m100) cc_final: 0.1296 (m100) REVERT: E 23 THR cc_start: 0.2525 (m) cc_final: 0.1896 (p) REVERT: E 213 PHE cc_start: -0.1076 (OUTLIER) cc_final: -0.2425 (m-80) REVERT: F 51 MET cc_start: 0.1920 (OUTLIER) cc_final: 0.1146 (ppp) REVERT: G 97 TYR cc_start: 0.0791 (OUTLIER) cc_final: -0.0397 (p90) REVERT: G 110 ILE cc_start: 0.1754 (OUTLIER) cc_final: 0.1438 (pt) REVERT: I 97 TYR cc_start: 0.0546 (OUTLIER) cc_final: -0.1294 (p90) outliers start: 110 outliers final: 71 residues processed: 345 average time/residue: 0.4371 time to fit residues: 261.6048 Evaluate side-chains 319 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 236 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 257 optimal weight: 0.0370 chunk 329 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 380 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 450 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN C1177 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37054 Z= 0.307 Angle : 0.750 13.900 50378 Z= 0.394 Chirality : 0.049 0.473 5675 Planarity : 0.005 0.093 6483 Dihedral : 6.515 56.284 5109 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.23 % Favored : 88.36 % Rotamer: Outliers : 2.99 % Allowed : 16.63 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4641 helix: 0.90 (0.19), residues: 731 sheet: -0.04 (0.15), residues: 1209 loop : -1.94 (0.11), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 35 HIS 0.009 0.002 HIS B1138 PHE 0.031 0.002 PHE A 778 TYR 0.047 0.002 TYR B 641 ARG 0.009 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 231 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6662 (m-10) cc_final: 0.6219 (m-80) REVERT: A 452 MET cc_start: 0.2243 (ptp) cc_final: 0.1436 (ptp) REVERT: A 455 ASP cc_start: 0.2414 (t0) cc_final: 0.1888 (m-30) REVERT: A 486 HIS cc_start: 0.4636 (OUTLIER) cc_final: 0.4114 (p-80) REVERT: A 629 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7677 (ttm-80) REVERT: A 796 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6176 (tp40) REVERT: A 960 TRP cc_start: 0.5217 (t-100) cc_final: 0.1651 (t-100) REVERT: A 988 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: B 161 MET cc_start: 0.6108 (mmp) cc_final: 0.5764 (mmt) REVERT: B 232 PHE cc_start: 0.7374 (m-80) cc_final: 0.6882 (t80) REVERT: B 1008 MET cc_start: 0.7722 (tmm) cc_final: 0.7440 (ttp) REVERT: B 1060 VAL cc_start: 0.6086 (m) cc_final: 0.5813 (p) REVERT: C 183 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6546 (p90) REVERT: C 960 TRP cc_start: 0.7264 (OUTLIER) cc_final: 0.5532 (t60) REVERT: C 1195 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: D 60 THR cc_start: 0.0554 (OUTLIER) cc_final: 0.0101 (t) REVERT: D 120 TRP cc_start: 0.1938 (m100) cc_final: 0.1399 (m100) REVERT: E 213 PHE cc_start: -0.0826 (OUTLIER) cc_final: -0.2160 (m-80) REVERT: F 51 MET cc_start: 0.1596 (OUTLIER) cc_final: 0.0889 (ppp) REVERT: G 97 TYR cc_start: 0.0774 (OUTLIER) cc_final: -0.0339 (p90) REVERT: G 110 ILE cc_start: 0.1500 (OUTLIER) cc_final: 0.1140 (pt) REVERT: I 97 TYR cc_start: 0.0665 (OUTLIER) cc_final: -0.1225 (p90) outliers start: 121 outliers final: 89 residues processed: 328 average time/residue: 0.4239 time to fit residues: 241.0415 Evaluate side-chains 324 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 222 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1163 ASN Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 135 optimal weight: 0.4980 chunk 88 optimal weight: 0.0020 chunk 87 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 68 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37054 Z= 0.164 Angle : 0.660 15.517 50378 Z= 0.341 Chirality : 0.045 0.318 5675 Planarity : 0.004 0.059 6483 Dihedral : 5.980 57.646 5109 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.79 % Favored : 90.91 % Rotamer: Outliers : 2.49 % Allowed : 17.10 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4641 helix: 1.27 (0.20), residues: 732 sheet: 0.07 (0.15), residues: 1224 loop : -1.85 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 35 HIS 0.004 0.001 HIS C 681 PHE 0.035 0.001 PHE B 423 TYR 0.037 0.001 TYR B 641 ARG 0.008 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 238 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6473 (m-10) cc_final: 0.6195 (m-80) REVERT: A 452 MET cc_start: 0.2210 (ptp) cc_final: 0.1914 (ptt) REVERT: A 455 ASP cc_start: 0.2295 (t0) cc_final: 0.1449 (m-30) REVERT: A 486 HIS cc_start: 0.4693 (OUTLIER) cc_final: 0.4146 (p-80) REVERT: A 629 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7479 (tpp80) REVERT: A 960 TRP cc_start: 0.5214 (t-100) cc_final: 0.1591 (t-100) REVERT: A 1112 LYS cc_start: 0.7552 (tppt) cc_final: 0.7098 (mmmt) REVERT: B 161 MET cc_start: 0.6140 (mmp) cc_final: 0.5651 (mmt) REVERT: B 1060 VAL cc_start: 0.5863 (m) cc_final: 0.5603 (p) REVERT: C 183 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6518 (p90) REVERT: C 563 MET cc_start: 0.2605 (mtt) cc_final: -0.0254 (ptp) REVERT: C 569 MET cc_start: 0.0602 (mtm) cc_final: -0.0667 (mmp) REVERT: C 865 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: C 960 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.5330 (t60) REVERT: C 1008 MET cc_start: 0.7531 (ttm) cc_final: 0.7292 (tpp) REVERT: C 1053 ASP cc_start: 0.7584 (m-30) cc_final: 0.7008 (p0) REVERT: C 1195 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: D 60 THR cc_start: 0.0766 (OUTLIER) cc_final: 0.0304 (t) REVERT: D 120 TRP cc_start: 0.2180 (m100) cc_final: 0.1659 (m100) REVERT: E 23 THR cc_start: 0.2378 (m) cc_final: 0.1741 (p) REVERT: E 213 PHE cc_start: -0.0937 (OUTLIER) cc_final: -0.2201 (m-80) REVERT: F 51 MET cc_start: 0.1557 (OUTLIER) cc_final: 0.0870 (ppp) REVERT: F 68 GLN cc_start: 0.3512 (OUTLIER) cc_final: 0.2295 (tm-30) REVERT: G 97 TYR cc_start: 0.0732 (OUTLIER) cc_final: -0.0574 (p90) REVERT: G 110 ILE cc_start: 0.1378 (OUTLIER) cc_final: 0.1109 (pt) REVERT: H 9 GLN cc_start: 0.1403 (OUTLIER) cc_final: 0.0968 (mp10) REVERT: I 97 TYR cc_start: 0.0347 (OUTLIER) cc_final: -0.1409 (p90) outliers start: 101 outliers final: 72 residues processed: 325 average time/residue: 0.4372 time to fit residues: 246.1006 Evaluate side-chains 314 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 228 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 794 TYR Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1184 TRP Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 0.7980 chunk 431 optimal weight: 0.8980 chunk 393 optimal weight: 2.9990 chunk 419 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 379 optimal weight: 3.9990 chunk 396 optimal weight: 0.7980 chunk 417 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1177 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37054 Z= 0.183 Angle : 0.656 15.352 50378 Z= 0.340 Chirality : 0.045 0.341 5675 Planarity : 0.004 0.061 6483 Dihedral : 5.932 56.514 5109 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.00 % Favored : 89.70 % Rotamer: Outliers : 2.42 % Allowed : 17.18 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 4641 helix: 1.27 (0.20), residues: 732 sheet: 0.11 (0.15), residues: 1203 loop : -1.81 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 35 HIS 0.005 0.001 HIS C 681 PHE 0.030 0.001 PHE B 423 TYR 0.046 0.001 TYR B1171 ARG 0.008 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 229 time to evaluate : 4.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.2164 (ptp) cc_final: 0.1819 (ptt) REVERT: A 455 ASP cc_start: 0.2329 (t0) cc_final: 0.1442 (m-30) REVERT: A 486 HIS cc_start: 0.4709 (OUTLIER) cc_final: 0.4103 (p-80) REVERT: A 629 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7634 (mmm-85) REVERT: A 960 TRP cc_start: 0.5281 (t-100) cc_final: 0.1662 (t-100) REVERT: A 1112 LYS cc_start: 0.7589 (tppt) cc_final: 0.7032 (mmmt) REVERT: B 161 MET cc_start: 0.6047 (mmp) cc_final: 0.5588 (mmt) REVERT: B 232 PHE cc_start: 0.7222 (m-80) cc_final: 0.6766 (t80) REVERT: B 1060 VAL cc_start: 0.5716 (m) cc_final: 0.5436 (p) REVERT: C 183 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6659 (p90) REVERT: C 224 SER cc_start: 0.7164 (m) cc_final: 0.6779 (t) REVERT: C 563 MET cc_start: 0.2830 (mtt) cc_final: -0.0036 (ptp) REVERT: C 569 MET cc_start: 0.0290 (mtm) cc_final: -0.0817 (mmp) REVERT: C 865 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: C 960 TRP cc_start: 0.7159 (OUTLIER) cc_final: 0.5431 (t60) REVERT: C 1012 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7684 (t80) REVERT: C 1053 ASP cc_start: 0.7562 (m-30) cc_final: 0.7077 (p0) REVERT: C 1195 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: D 60 THR cc_start: 0.0788 (OUTLIER) cc_final: 0.0335 (t) REVERT: D 120 TRP cc_start: 0.2346 (m100) cc_final: 0.1820 (m100) REVERT: E 213 PHE cc_start: -0.0958 (OUTLIER) cc_final: -0.2246 (m-80) REVERT: F 49 GLU cc_start: 0.2535 (tp30) cc_final: 0.1591 (tt0) REVERT: F 51 MET cc_start: 0.1838 (OUTLIER) cc_final: 0.0932 (ppp) REVERT: F 84 MET cc_start: 0.0614 (tpp) cc_final: -0.0260 (tmm) REVERT: G 97 TYR cc_start: 0.0672 (OUTLIER) cc_final: -0.0639 (p90) REVERT: G 110 ILE cc_start: 0.1386 (OUTLIER) cc_final: 0.1107 (pt) REVERT: I 97 TYR cc_start: 0.0218 (OUTLIER) cc_final: -0.1512 (p90) outliers start: 98 outliers final: 77 residues processed: 313 average time/residue: 0.4215 time to fit residues: 229.8967 Evaluate side-chains 312 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 222 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1186 TYR Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 9 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 3.9990 chunk 443 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 308 optimal weight: 0.0170 chunk 465 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 286 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 overall best weight: 3.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1160 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 37054 Z= 0.375 Angle : 0.799 15.104 50378 Z= 0.421 Chirality : 0.050 0.441 5675 Planarity : 0.006 0.076 6483 Dihedral : 6.706 59.733 5107 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.74 % Favored : 87.89 % Rotamer: Outliers : 2.34 % Allowed : 17.35 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4641 helix: 0.74 (0.19), residues: 737 sheet: -0.16 (0.15), residues: 1232 loop : -2.01 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 50 HIS 0.012 0.002 HIS C 681 PHE 0.040 0.003 PHE B 764 TYR 0.052 0.003 TYR B 641 ARG 0.008 0.001 ARG C1113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 222 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.2224 (ptp) cc_final: 0.2010 (ptt) REVERT: A 455 ASP cc_start: 0.2642 (t0) cc_final: 0.2076 (m-30) REVERT: A 486 HIS cc_start: 0.4806 (OUTLIER) cc_final: 0.4053 (p-80) REVERT: A 629 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: B 161 MET cc_start: 0.5992 (mmp) cc_final: 0.5549 (mmt) REVERT: B 232 PHE cc_start: 0.7287 (m-80) cc_final: 0.6837 (t80) REVERT: C 180 LEU cc_start: 0.7893 (tt) cc_final: 0.7674 (tp) REVERT: C 183 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6580 (p90) REVERT: C 224 SER cc_start: 0.6949 (m) cc_final: 0.6436 (t) REVERT: C 231 TYR cc_start: 0.6925 (m-80) cc_final: 0.6669 (m-80) REVERT: C 865 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: C 960 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.5355 (t60) REVERT: C 1012 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7996 (t80) REVERT: C 1195 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: D 60 THR cc_start: 0.0296 (OUTLIER) cc_final: -0.0061 (t) REVERT: E 213 PHE cc_start: -0.0859 (OUTLIER) cc_final: -0.2279 (m-80) REVERT: F 49 GLU cc_start: 0.2638 (tp30) cc_final: 0.1734 (tt0) REVERT: F 51 MET cc_start: 0.1605 (OUTLIER) cc_final: 0.0831 (ppp) REVERT: G 97 TYR cc_start: 0.0461 (OUTLIER) cc_final: -0.0446 (p90) REVERT: G 110 ILE cc_start: 0.1309 (OUTLIER) cc_final: 0.1036 (pt) REVERT: I 97 TYR cc_start: 0.0413 (OUTLIER) cc_final: -0.1454 (p90) outliers start: 95 outliers final: 74 residues processed: 303 average time/residue: 0.4716 time to fit residues: 252.2811 Evaluate side-chains 297 residues out of total 4054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 210 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 713 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1106 CYS Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 1125 SER Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 865 PHE Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1195 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain F residue 51 MET Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain G residue 97 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 213 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 0.3980 chunk 394 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 341 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 371 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN B 681 HIS ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN C 236 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.142056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.106046 restraints weight = 212973.533| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 5.85 r_work: 0.3378 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 37054 Z= 0.429 Angle : 0.851 16.070 50378 Z= 0.449 Chirality : 0.053 0.477 5675 Planarity : 0.006 0.074 6483 Dihedral : 7.263 56.911 5107 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.03 % Favored : 87.61 % Rotamer: Outliers : 2.47 % Allowed : 17.55 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4641 helix: 0.60 (0.19), residues: 731 sheet: -0.50 (0.15), residues: 1246 loop : -2.23 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 50 HIS 0.011 0.002 HIS C 681 PHE 0.041 0.003 PHE B 764 TYR 0.053 0.003 TYR A1192 ARG 0.008 0.001 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9225.83 seconds wall clock time: 167 minutes 29.96 seconds (10049.96 seconds total)