Starting phenix.real_space_refine (version: dev) on Tue Feb 21 09:57:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lok_23465/02_2023/7lok_23465_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 97": "NH1" <-> "NH2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M ASP 110": "OD1" <-> "OD2" Residue "M PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14498 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2802 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2832 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "K" Number of atoms: 999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1014 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 835 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} bond proxies already assigned to first conformer: 1014 Chain: "G" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 209 Unusual residues: {'MPT': 1, 'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 24, None: 1} Not linked: pdbres="MPT G 1 " pdbres="ASN G 2 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MPT:plan-1': 1, 'U2X:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 209 Unusual residues: {'MPT': 1, 'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 24, None: 1} Not linked: pdbres="MPT H 1 " pdbres="ASN H 2 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MPT:plan-1': 1, 'U2X:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 631 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 238 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1751 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1400 Unresolved non-hydrogen dihedrals: 911 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 25, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 13, 'GLU:plan': 19, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 560 Chain: "I" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 149 Unusual residues: {'MPT': 1, 'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 2} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 24, None: 1} Not linked: pdbres="MPT I 1 " pdbres="ASN I 2 " Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'MPT:plan-1': 1, 'U2X:plan-2': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LYS G 11 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS G 11 " occ=0.50 residue: pdb=" N LYS H 11 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS H 11 " occ=0.50 residue: pdb=" N LYS I 11 " occ=0.50 ... (3 atoms not shown) pdb=" CB LYS I 11 " occ=0.50 Time building chain proxies: 9.30, per 1000 atoms: 0.64 Number of scatterers: 14498 At special positions: 0 Unit cell: (135.792, 138, 149.04, 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 84 16.00 O 2818 8.00 N 2558 7.00 C 9038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 385 " distance=2.01 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.29 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 26 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 24 " distance=2.03 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS H 26 " distance=2.03 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=4, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 295 " " NAG C 601 " - " ASN C 448 " " NAG E 601 " - " ASN E 295 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN E 262 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPR G 21 " pdb=" CB DPR H 21 " pdb=" CB DPR I 21 " Number of C-beta restraints generated: 3710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 32 sheets defined 18.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 100 through 115 removed outlier: 4.016A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 4.250A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'D' and resid 517 through 525 removed outlier: 4.524A pdb=" N ALA D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 4.182A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 4.606A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 590 removed outlier: 3.846A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 628 through 635 removed outlier: 3.779A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.916A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 338 through 352 removed outlier: 4.102A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'B' and resid 522 through 525 removed outlier: 3.987A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 530 through 541 Processing helix chain 'B' and resid 563 through 566 No H-bonds generated for 'chain 'B' and resid 563 through 566' Processing helix chain 'B' and resid 573 through 582 removed outlier: 4.584A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 592 removed outlier: 3.518A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.758A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 655 removed outlier: 5.637A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 643 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 646 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER B 649 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 652 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 104 through 106 No H-bonds generated for 'chain 'K' and resid 104 through 106' Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'G' and resid 3 through 13 Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.666A pdb=" N ARG H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS H 10 " --> pdb=" O CYS H 6 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 12 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU H 13 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 522 No H-bonds generated for 'chain 'F' and resid 519 through 522' Processing helix chain 'F' and resid 530 through 545 removed outlier: 4.154A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 596 removed outlier: 4.467A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 623 No H-bonds generated for 'chain 'F' and resid 621 through 623' Processing helix chain 'F' and resid 628 through 635 removed outlier: 4.629A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 653 removed outlier: 4.046A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 69 No H-bonds generated for 'chain 'E' and resid 66 through 69' Processing helix chain 'E' and resid 101 through 113 removed outlier: 4.616A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 removed outlier: 3.764A pdb=" N LYS E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.576A pdb=" N SER I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU I 13 " --> pdb=" O ARG I 9 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.682A pdb=" N SER C 243 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.641A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.671A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 449 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.714A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= G, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= H, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.569A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= J, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.547A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.754A pdb=" N ILE A 201 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 123 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 199 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 443 through 446 removed outlier: 3.837A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 414 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.618A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER J 63 " --> pdb=" O THR J 74 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.557A pdb=" N ARG J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'J' and resid 85 through 90 removed outlier: 3.566A pdb=" N TRP J 35 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= Q, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.647A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 68 through 73 removed outlier: 3.991A pdb=" N THR K 71 " --> pdb=" O TYR K 80 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.795A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.301A pdb=" N ARG L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'L' and resid 85 through 89 removed outlier: 3.632A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.592A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 10 through 12 Processing sheet with id= X, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.817A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 93 through 100 removed outlier: 3.695A pdb=" N VAL M 99 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP M 36 " --> pdb=" O GLY M 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.886A pdb=" N THR E 37 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 497 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.719A pdb=" N LYS E 490 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= AC, first strand: chain 'E' and resid 83 through 85 Processing sheet with id= AD, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.098A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.736A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 423 through 425 removed outlier: 4.132A pdb=" N ILE E 424 " --> pdb=" O ALA E 433 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 7.11 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: 2441 1.31 - 1.45: 3961 1.45 - 1.58: 8235 1.58 - 1.71: 2 1.71 - 1.85: 108 Bond restraints: 14747 Sorted by residual: bond pdb=" C VAL H 27 " pdb=" N NH2 H 28 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" C VAL G 27 " pdb=" N NH2 G 28 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" C VAL I 27 " pdb=" N NH2 I 28 " ideal model delta sigma weight residual 1.329 1.429 -0.100 1.40e-02 5.10e+03 5.15e+01 bond pdb=" C1 NAG O 1 " pdb=" C2 NAG O 1 " ideal model delta sigma weight residual 1.526 1.651 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CD2 U2X I 23 " pdb=" CE2 U2X I 23 " ideal model delta sigma weight residual 1.390 1.513 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 14742 not shown) Histogram of bond angle deviations from ideal: 54.05 - 74.61: 1 74.61 - 95.17: 4 95.17 - 115.74: 9786 115.74 - 136.30: 10301 136.30 - 156.86: 1 Bond angle restraints: 20093 Sorted by residual: angle pdb=" O VAL G 27 " pdb=" C VAL G 27 " pdb=" N NH2 G 28 " ideal model delta sigma weight residual 123.00 54.05 68.95 1.60e+00 3.91e-01 1.86e+03 angle pdb=" O VAL H 27 " pdb=" C VAL H 27 " pdb=" N NH2 H 28 " ideal model delta sigma weight residual 123.00 156.86 -33.86 1.60e+00 3.91e-01 4.48e+02 angle pdb=" CA VAL H 27 " pdb=" C VAL H 27 " pdb=" N NH2 H 28 " ideal model delta sigma weight residual 116.20 75.24 40.96 2.00e+00 2.50e-01 4.19e+02 angle pdb=" CA VAL G 27 " pdb=" C VAL G 27 " pdb=" N NH2 G 28 " ideal model delta sigma weight residual 116.20 75.41 40.79 2.00e+00 2.50e-01 4.16e+02 angle pdb=" C2 NAG O 1 " pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 109.64 101.12 8.52 5.38e-01 3.45e+00 2.51e+02 ... (remaining 20088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7998 17.95 - 35.91: 645 35.91 - 53.86: 98 53.86 - 71.82: 18 71.82 - 89.77: 13 Dihedral angle restraints: 8772 sinusoidal: 3042 harmonic: 5730 Sorted by residual: dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 24 " pdb=" CB CYS G 24 " ideal model delta sinusoidal sigma weight residual -86.00 -174.40 88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -9.70 -76.30 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -12.36 -73.64 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 8769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 2393 0.269 - 0.539: 3 0.539 - 0.808: 2 0.808 - 1.077: 1 1.077 - 1.346: 1 Chirality restraints: 2400 Sorted by residual: chirality pdb=" C1 MAN N 6 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 6 " pdb=" O5 MAN N 6 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.53e+03 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 7.04e+01 chirality pdb=" C1 MAN O 5 " pdb=" O3 MAN O 4 " pdb=" C2 MAN O 5 " pdb=" O5 MAN O 5 " both_signs ideal model delta sigma weight residual False 2.40 2.24 0.16 2.00e-02 2.50e+03 6.54e+01 ... (remaining 2397 not shown) Planarity restraints: 2598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 605 " 0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A 605 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 605 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG A 605 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG A 605 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.263 2.00e-02 2.50e+03 2.22e-01 6.15e+02 pdb=" C7 NAG O 1 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.247 2.00e-02 2.50e+03 2.12e-01 5.64e+02 pdb=" C7 NAG N 2 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.186 2.00e-02 2.50e+03 ... (remaining 2595 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 12 1.96 - 2.70: 714 2.70 - 3.43: 19861 3.43 - 4.17: 30265 4.17 - 4.90: 52198 Nonbonded interactions: 103050 Sorted by model distance: nonbonded pdb=" O DPR G 21 " pdb=" N U2X G 23 " model vdw 1.226 2.520 nonbonded pdb=" O DPR H 21 " pdb=" N U2X H 23 " model vdw 1.263 2.520 nonbonded pdb=" C DPR H 21 " pdb=" N U2X H 23 " model vdw 1.451 3.350 nonbonded pdb=" C DPR G 21 " pdb=" N U2X G 23 " model vdw 1.453 3.350 nonbonded pdb=" N LEU F 523 " pdb=" CB PRO E 43 " model vdw 1.480 3.520 ... (remaining 103045 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 34 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 or (resid 42 through 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or (resid 197 through 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 or (resid 223 through 234 and (n \ ame N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 or (resid 23 \ 8 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 or (resid 251 through 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 263 or (resid 264 through 294 and (name N or name CA \ or name C or name O or name CB )) or resid 295 or (resid 296 through 342 and (n \ ame N or name CA or name C or name O or name CB )) or resid 343 or (resid 344 th \ rough 353 and (name N or name CA or name C or name O or name CB )) or resid 354 \ or (resid 355 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 367 or (resid 368 through 378 and (name N or name CA or \ name C or name O or name CB )) or (resid 379 through 388 and (name N or name CA \ or name C or name O or name CB )) or resid 389 or (resid 390 through 430 and (na \ me N or name CA or name C or name O or name CB )) or resid 431 or (resid 432 thr \ ough 440 and (name N or name CA or name C or name O or name CB )) or resid 441 o \ r (resid 442 through 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 451 or (resid 452 through 457 and (name N or name CA or name C or nam \ e O or name CB )) or resid 458 or (resid 464 through 470 and (name N or name CA \ or name C or name O or name CB )) or resid 471 through 473 or (resid 474 through \ 494 and (name N or name CA or name C or name O or name CB )) or resid 495 or (r \ esid 496 through 499 and (name N or name CA or name C or name O or name CB )) or \ resid 606)) selection = (chain 'C' and ((resid 34 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 or (resid 42 through 123 and (name N or name CA or nam \ e C or name O or name CB )) or resid 124 or (resid 125 and (name N or name CA or \ name C or name O or name CB )) or (resid 197 through 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 or (resid 223 through 234 and (n \ ame N or name CA or name C or name O or name CB )) or resid 235 or (resid 236 an \ d (name N or name CA or name C or name O or name CB )) or resid 237 or (resid 23 \ 8 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 or (resid 251 through 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 263 or (resid 264 through 294 and (name N or name CA \ or name C or name O or name CB )) or resid 295 or (resid 296 through 300 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 326 through 342 and \ (name N or name CA or name C or name O or name CB )) or resid 343 or (resid 344 \ through 353 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 54 or (resid 355 through 365 and (name N or name CA or name C or name O or name \ CB )) or resid 366 through 367 or (resid 368 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 through 380 or (resid 381 through \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 or (r \ esid 390 through 430 and (name N or name CA or name C or name O or name CB )) or \ resid 431 or (resid 432 through 440 and (name N or name CA or name C or name O \ or name CB )) or resid 441 or (resid 442 through 450 and (name N or name CA or n \ ame C or name O or name CB )) or resid 451 or (resid 452 through 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 or (resid 464 through \ 470 and (name N or name CA or name C or name O or name CB )) or resid 471 throu \ gh 473 or (resid 474 through 494 and (name N or name CA or name C or name O or n \ ame CB )) or resid 495 or (resid 496 through 499 and (name N or name CA or name \ C or name O or name CB )) or resid 601)) selection = (chain 'E' and (resid 34 through 458 or resid 464 through 499 or resid 601)) } ncs_group { reference = (chain 'B' and ((resid 519 through 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 or (resid 522 through 523 and (name N or name CA or \ name C or name O or name CB )) or (resid 524 through 530 and (name N or name CA \ or name C or name O or name CB )) or (resid 531 through 542 and (name N or name \ CA or name C or name O or name CB )) or (resid 563 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 or (resid 573 through 593 \ and (name N or name CA or name C or name O or name CB )) or resid 594 or (resid \ 595 through 596 and (name N or name CA or name C or name O or name CB )) or resi \ d 597 or (resid 598 through 599 and (name N or name CA or name C or name O or na \ me CB )) or resid 600 or (resid 601 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 through 655 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 519 through 520 and (name N or name CA or name C or name \ O or name CB )) or resid 521 or (resid 522 through 523 and (name N or name CA or \ name C or name O or name CB )) or (resid 524 through 530 and (name N or name CA \ or name C or name O or name CB )) or (resid 531 through 542 and (name N or name \ CA or name C or name O or name CB )) or (resid 563 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 or (resid 573 through 593 \ and (name N or name CA or name C or name O or name CB )) or resid 594 or (resid \ 595 through 596 and (name N or name CA or name C or name O or name CB )) or resi \ d 597 or (resid 598 through 599 and (name N or name CA or name C or name O or na \ me CB )) or resid 600 or (resid 601 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 through 655 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 519 through 542 or resid 563 through 655)) } ncs_group { reference = (chain 'G' and ((resid 1 and (name CA or name C or name O or name CB )) or (resi \ d 2 through 13 and (name N or name CA or name C or name O or name CB )) or resid \ 14 or (resid 15 through 16 and (name N or name CA or name C or name O or name C \ B )) or resid 17 or (resid 18 through 20 and (name N or name CA or name C or nam \ e O or name CB )) or resid 21 or (resid 22 and (name N or name CA or name C or n \ ame O or name CB )) or resid 23 or (resid 24 through 27 and (name N or name CA o \ r name C or name O or name CB )) or resid 28)) selection = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB )) or (resi \ d 2 through 13 and (name N or name CA or name C or name O or name CB )) or resid \ 14 or (resid 15 through 16 and (name N or name CA or name C or name O or name C \ B )) or resid 17 or (resid 18 through 20 and (name N or name CA or name C or nam \ e O or name CB )) or resid 21 or (resid 22 and (name N or name CA or name C or n \ ame O or name CB )) or resid 23 or (resid 24 through 27 and (name N or name CA o \ r name C or name O or name CB )) or resid 28)) selection = chain 'I' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 3 through 108) } ncs_group { reference = (chain 'K' and (resid 1 through 42 or resid 44 through 129)) selection = (chain 'M' and (resid 1 through 42 or resid 44 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9038 2.51 5 N 2558 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.240 Process input model: 40.210 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.006 0.125 14747 Z= 0.438 Angle : 1.129 68.951 20093 Z= 0.665 Chirality : 0.068 1.346 2400 Planarity : 0.012 0.295 2587 Dihedral : 13.501 89.770 4978 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.86 % Favored : 87.99 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 4.60 % 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: -5.60 (0.14), residues: 1931 helix: -3.94 (0.15), residues: 385 sheet: -3.11 (0.20), residues: 505 loop : -4.05 (0.14), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 1.732 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 outliers start: 5 outliers final: 1 residues processed: 242 average time/residue: 0.2918 time to fit residues: 100.3598 Evaluate side-chains 167 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1223 time to fit residues: 2.4370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 174 optimal weight: 40.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS C 422 GLN D 543 ASN D 630 GLN A 33 ASN A 66 HIS A 72 HIS A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 37 GLN M 65 GLN H 4 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 14747 Z= 0.351 Angle : 0.725 20.188 20093 Z= 0.376 Chirality : 0.048 0.342 2400 Planarity : 0.005 0.069 2587 Dihedral : 6.468 73.877 2294 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.36 % Favored : 89.59 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -4.71 (0.16), residues: 1931 helix: -2.90 (0.20), residues: 397 sheet: -2.64 (0.22), residues: 500 loop : -3.55 (0.15), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.760 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 outliers start: 32 outliers final: 21 residues processed: 209 average time/residue: 0.2596 time to fit residues: 80.8484 Evaluate side-chains 187 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1266 time to fit residues: 7.2678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 174 optimal weight: 40.0000 chunk 188 optimal weight: 0.0050 chunk 155 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN D 543 ASN ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 14747 Z= 0.254 Angle : 0.633 18.185 20093 Z= 0.327 Chirality : 0.046 0.256 2400 Planarity : 0.004 0.075 2587 Dihedral : 6.013 70.440 2294 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.87 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.05 (0.17), residues: 1931 helix: -2.15 (0.23), residues: 396 sheet: -2.39 (0.22), residues: 496 loop : -3.13 (0.17), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.747 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 outliers start: 34 outliers final: 15 residues processed: 212 average time/residue: 0.2921 time to fit residues: 90.7842 Evaluate side-chains 181 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1282 time to fit residues: 5.9529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 185 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 14747 Z= 0.358 Angle : 0.678 18.166 20093 Z= 0.349 Chirality : 0.047 0.332 2400 Planarity : 0.004 0.065 2587 Dihedral : 6.149 68.265 2294 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.82 % Favored : 89.12 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.83 (0.17), residues: 1931 helix: -1.96 (0.23), residues: 399 sheet: -2.32 (0.23), residues: 482 loop : -2.95 (0.17), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.747 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 outliers start: 41 outliers final: 27 residues processed: 201 average time/residue: 0.2640 time to fit residues: 78.4183 Evaluate side-chains 189 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1293 time to fit residues: 8.9480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 14747 Z= 0.365 Angle : 0.672 18.223 20093 Z= 0.347 Chirality : 0.047 0.368 2400 Planarity : 0.004 0.059 2587 Dihedral : 6.317 73.401 2294 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.89 % Favored : 90.06 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.18), residues: 1931 helix: -1.82 (0.24), residues: 394 sheet: -2.24 (0.23), residues: 483 loop : -2.87 (0.17), residues: 1054 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.754 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 outliers start: 40 outliers final: 21 residues processed: 202 average time/residue: 0.2707 time to fit residues: 81.1538 Evaluate side-chains 178 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1336 time to fit residues: 7.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.5980 chunk 167 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 14747 Z= 0.344 Angle : 0.678 18.284 20093 Z= 0.345 Chirality : 0.047 0.375 2400 Planarity : 0.004 0.056 2587 Dihedral : 6.271 76.700 2294 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.10 % Favored : 89.85 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.18), residues: 1931 helix: -1.68 (0.24), residues: 397 sheet: -2.22 (0.23), residues: 492 loop : -2.80 (0.18), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 189 average time/residue: 0.2742 time to fit residues: 76.5631 Evaluate side-chains 170 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1380 time to fit residues: 6.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 72 HIS C 279 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.110 14747 Z= 0.737 Angle : 0.939 18.203 20093 Z= 0.486 Chirality : 0.056 0.525 2400 Planarity : 0.006 0.056 2587 Dihedral : 7.299 80.910 2294 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.54 % Favored : 84.41 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.17), residues: 1931 helix: -2.24 (0.22), residues: 417 sheet: -2.43 (0.22), residues: 514 loop : -3.23 (0.17), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 177 average time/residue: 0.2497 time to fit residues: 66.8958 Evaluate side-chains 164 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1356 time to fit residues: 7.6085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 168 optimal weight: 40.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 66 HIS C 279 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 14747 Z= 0.220 Angle : 0.659 18.439 20093 Z= 0.335 Chirality : 0.046 0.336 2400 Planarity : 0.004 0.052 2587 Dihedral : 6.334 78.466 2294 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.18), residues: 1931 helix: -1.54 (0.24), residues: 403 sheet: -2.18 (0.23), residues: 498 loop : -2.83 (0.18), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 185 average time/residue: 0.2794 time to fit residues: 75.4979 Evaluate side-chains 164 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1244 time to fit residues: 3.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 0.0670 chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 163 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 3.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 14747 Z= 0.412 Angle : 0.747 18.336 20093 Z= 0.380 Chirality : 0.049 0.400 2400 Planarity : 0.004 0.055 2587 Dihedral : 6.518 78.791 2294 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.53 % Favored : 87.42 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.18), residues: 1931 helix: -1.55 (0.24), residues: 417 sheet: -2.13 (0.23), residues: 498 loop : -2.92 (0.18), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 166 average time/residue: 0.2724 time to fit residues: 67.1891 Evaluate side-chains 161 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1325 time to fit residues: 4.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 40.0000 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 40.0000 chunk 176 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 93 optimal weight: 0.0060 chunk 120 optimal weight: 4.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14747 Z= 0.228 Angle : 0.673 18.428 20093 Z= 0.338 Chirality : 0.046 0.317 2400 Planarity : 0.004 0.052 2587 Dihedral : 6.179 77.152 2294 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.91 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.18), residues: 1931 helix: -1.20 (0.26), residues: 401 sheet: -2.02 (0.23), residues: 494 loop : -2.72 (0.18), residues: 1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 0.2816 time to fit residues: 70.2553 Evaluate side-chains 165 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1271 time to fit residues: 2.8251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.0770 chunk 133 optimal weight: 5.9990 overall best weight: 0.4540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.111079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087958 restraints weight = 73481.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088733 restraints weight = 51149.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089741 restraints weight = 37526.139| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14747 Z= 0.174 Angle : 0.628 18.449 20093 Z= 0.312 Chirality : 0.045 0.263 2400 Planarity : 0.004 0.061 2587 Dihedral : 5.638 74.110 2294 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.60 % 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: -2.93 (0.18), residues: 1931 helix: -0.86 (0.26), residues: 395 sheet: -1.69 (0.23), residues: 499 loop : -2.56 (0.18), residues: 1037 =============================================================================== Job complete usr+sys time: 2476.97 seconds wall clock time: 45 minutes 56.98 seconds (2756.98 seconds total)