Starting phenix.real_space_refine on Sun Nov 17 07:44:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i10_35115/11_2024/8i10_35115.cif" } resolution = 3.96 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= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 24 5.16 5 C 8375 2.51 5 N 2264 2.21 5 O 2518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13196 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2641 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2632 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2603 Classifications: {'peptide': 343} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 908 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 786 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.73, per 1000 atoms: 0.74 Number of scatterers: 13196 At special positions: 0 Unit cell: (149.274, 143.443, 90.9636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 15 15.00 O 2518 8.00 N 2264 7.00 C 8375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 33 sheets defined 3.7% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.720A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.658A pdb=" N ARG B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.776A pdb=" N ARG C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.648A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.536A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.515A pdb=" N PHE A 342 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 258 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 234 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 236 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 116 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.871A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.595A pdb=" N LYS B 78 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 63 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 88 removed outlier: 5.540A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 63 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 128 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.565A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.176A pdb=" N PHE C 28 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 169 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL C 56 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS C 78 " --> pdb=" O PHE C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 190 Processing sheet with id=AB7, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.523A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.311A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.311A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.655A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.608A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC6, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.689A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.689A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.781A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.921A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 6 through 10 Processing sheet with id=AD3, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.366A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.366A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ARG M 103 " --> pdb=" O LEU M 110 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU M 110 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD6, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.605A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR N 103 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1272 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: 4.23 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4025 1.33 - 1.46: 3142 1.46 - 1.58: 6265 1.58 - 1.71: 39 1.71 - 1.83: 33 Bond restraints: 13504 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.597 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" OG1 TPO U 360 " pdb=" P TPO U 360 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 13499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17521 2.00 - 3.99: 727 3.99 - 5.99: 112 5.99 - 7.98: 28 7.98 - 9.98: 15 Bond angle restraints: 18403 Sorted by residual: angle pdb=" C SEP V 363 " pdb=" N SEP V 364 " pdb=" CA SEP V 364 " ideal model delta sigma weight residual 121.70 111.72 9.98 1.80e+00 3.09e-01 3.07e+01 angle pdb=" N SER B 75 " pdb=" CA SER B 75 " pdb=" C SER B 75 " ideal model delta sigma weight residual 110.80 120.21 -9.41 2.13e+00 2.20e-01 1.95e+01 angle pdb=" CA GLN C 182 " pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA LYS A 108 " pdb=" CB LYS A 108 " pdb=" CG LYS A 108 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA LEU V 365 " pdb=" C LEU V 365 " pdb=" N ALA V 366 " ideal model delta sigma weight residual 116.20 124.15 -7.95 2.00e+00 2.50e-01 1.58e+01 ... (remaining 18398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7353 17.93 - 35.86: 585 35.86 - 53.79: 85 53.79 - 71.72: 15 71.72 - 89.65: 19 Dihedral angle restraints: 8057 sinusoidal: 3026 harmonic: 5031 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA THR N 98 " pdb=" C THR N 98 " pdb=" N PHE N 99 " pdb=" CA PHE N 99 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LEU C 74 " pdb=" C LEU C 74 " pdb=" N SER C 75 " pdb=" CA SER C 75 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 8054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1718 0.070 - 0.141: 332 0.141 - 0.211: 30 0.211 - 0.281: 7 0.281 - 0.351: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CG LEU B 49 " pdb=" CB LEU B 49 " pdb=" CD1 LEU B 49 " pdb=" CD2 LEU B 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU M 21 " pdb=" CB LEU M 21 " pdb=" CD1 LEU M 21 " pdb=" CD2 LEU M 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2086 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 71 " 0.036 2.00e-02 2.50e+03 3.91e-02 2.67e+01 pdb=" CG PHE H 71 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE H 71 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 71 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE H 71 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE H 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 71 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 71 " 0.028 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE D 71 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 71 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 71 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE D 71 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE D 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 71 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 209 " 0.015 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR A 209 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 209 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 209 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 209 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 209 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 209 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 209 " -0.003 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 719 2.72 - 3.26: 13252 3.26 - 3.81: 19584 3.81 - 4.35: 23366 4.35 - 4.90: 42287 Nonbonded interactions: 99208 Sorted by model distance: nonbonded pdb=" O SER L 29 " pdb=" OG SER L 29 " model vdw 2.172 3.040 nonbonded pdb=" O SER M 34 " pdb=" OG SER M 34 " model vdw 2.211 3.040 nonbonded pdb=" O ASN D 31 " pdb=" OG SER D 35 " model vdw 2.222 3.040 nonbonded pdb=" NZ LYS C 108 " pdb=" OG SEP V 363 " model vdw 2.266 3.120 nonbonded pdb=" O SER E 32 " pdb=" OG SER E 32 " model vdw 2.268 3.040 ... (remaining 99203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 49 or (resid 50 and \ (name N or name CA or name C or name O )) or (resid 51 and (name N or name CA or \ name C or name O or name CB )) or resid 52 through 73 or (resid 74 through 76 a \ nd (name N or name CA or name C or name O or name CB )) or resid 77 through 84 o \ r (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 \ through 102 or (resid 103 and (name N or name CA or name C or name O or name CB \ )) or resid 104 through 110 or (resid 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 185 or (resid 186 and ( \ name N or name CA or name C or name O or name CB )) or resid 187 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 283 or (resid 284 and (name N or name CA or name C or name O or name CB \ )) or resid 285 through 295 or (resid 296 and (name N or name CA or name C or n \ ame O or name CB )) or resid 297 through 311 or (resid 312 and (name N or name C \ A or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and ( \ name N or name CA or name C or name O or name CB )) or resid 316 through 350)) selection = (chain 'B' and (resid 7 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or (resid 51 and (name N or name CA or name C or name \ O or name CB )) or resid 52 through 75 or (resid 76 and (name N or name CA or n \ ame C or name O or name CB )) or resid 77 through 84 or (resid 85 and (name N or \ name CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 \ and (name N or name CA or name C or name O or name CB )) or resid 104 through 1 \ 10 or (resid 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 113 or (resid 114 and (name N or name CA or name C or name O or n \ ame CB )) or resid 115 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 156 or (resid 157 through 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 176 o \ r (resid 177 through 178 and (name N or name CA or name C or name O or name CB ) \ ) or resid 179 through 229 or (resid 230 and (name N or name CA or name C or nam \ e O or name CB )) or resid 231 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 through 350)) selection = (chain 'C' and (resid 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 92 or (resid 93 and (n \ ame N or name CA or name C or name O or name CB )) or resid 94 through 176 or (r \ esid 177 through 178 and (name N or name CA or name C or name O or name CB )) or \ resid 179 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 229 or (resid 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 311 or (resid \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 45 or (resid 46 and (name \ N or name CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'H' and (resid 5 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 45 or (resid 46 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'M' and resid 5 through 121) } ncs_group { reference = (chain 'E' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'L' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'N' and resid 2 through 106) } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.020 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 0.120 13504 Z= 0.384 Angle : 0.951 9.977 18403 Z= 0.486 Chirality : 0.055 0.351 2089 Planarity : 0.007 0.063 2344 Dihedral : 13.994 89.646 4805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.58 % Allowed : 16.20 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % 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: -1.07 (0.20), residues: 1681 helix: -0.54 (0.80), residues: 36 sheet: -0.41 (0.18), residues: 769 loop : -0.92 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 36 HIS 0.011 0.002 HIS B 112 PHE 0.089 0.003 PHE H 71 TYR 0.061 0.003 TYR A 209 ARG 0.009 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: H 80 ASN cc_start: 0.7625 (t0) cc_final: 0.7362 (t0) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 0.2477 time to fit residues: 66.2973 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0370 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 160 HIS A 199 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 182 GLN B 199 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 42 GLN H 85 GLN M 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13504 Z= 0.202 Angle : 0.676 9.822 18403 Z= 0.345 Chirality : 0.047 0.174 2089 Planarity : 0.005 0.059 2344 Dihedral : 6.997 89.274 1921 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.54 % Allowed : 15.04 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1681 helix: 0.69 (0.86), residues: 36 sheet: 0.04 (0.19), residues: 746 loop : -0.90 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 50 HIS 0.005 0.001 HIS A 346 PHE 0.026 0.002 PHE C 278 TYR 0.017 0.002 TYR N 92 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.557 Fit side-chains REVERT: A 39 ASP cc_start: 0.8453 (p0) cc_final: 0.8131 (p0) REVERT: A 88 PHE cc_start: 0.6853 (t80) cc_final: 0.6645 (t80) REVERT: B 88 PHE cc_start: 0.7467 (t80) cc_final: 0.7180 (t80) REVERT: B 296 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7223 (m-70) REVERT: C 39 ASP cc_start: 0.8756 (p0) cc_final: 0.8532 (p0) REVERT: C 266 SER cc_start: 0.7998 (m) cc_final: 0.7672 (p) REVERT: C 324 VAL cc_start: 0.8935 (t) cc_final: 0.8603 (m) REVERT: D 9 GLU cc_start: 0.7239 (pm20) cc_final: 0.6927 (pt0) REVERT: D 81 THR cc_start: 0.8494 (m) cc_final: 0.8204 (p) REVERT: E 64 SER cc_start: 0.8301 (p) cc_final: 0.7711 (m) REVERT: L 5 MET cc_start: 0.8277 (tpp) cc_final: 0.7479 (tpp) REVERT: L 13 SER cc_start: 0.8364 (t) cc_final: 0.7951 (m) REVERT: M 21 LEU cc_start: 0.7648 (tp) cc_final: 0.7002 (tt) REVERT: N 6 THR cc_start: 0.8649 (t) cc_final: 0.8418 (p) outliers start: 49 outliers final: 29 residues processed: 218 average time/residue: 0.2240 time to fit residues: 74.7656 Evaluate side-chains 184 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.0980 chunk 51 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS C 160 HIS H 85 GLN M 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13504 Z= 0.184 Angle : 0.619 9.159 18403 Z= 0.315 Chirality : 0.045 0.159 2089 Planarity : 0.005 0.052 2344 Dihedral : 6.458 88.975 1913 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.75 % Allowed : 17.28 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1681 helix: 1.60 (0.88), residues: 36 sheet: 0.16 (0.19), residues: 750 loop : -0.76 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 39 HIS 0.004 0.001 HIS A 211 PHE 0.016 0.001 PHE C 278 TYR 0.013 0.001 TYR M 98 ARG 0.006 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.611 Fit side-chains REVERT: A 39 ASP cc_start: 0.8511 (p0) cc_final: 0.8199 (p0) REVERT: B 88 PHE cc_start: 0.7400 (t80) cc_final: 0.7141 (t80) REVERT: B 296 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7376 (m-70) REVERT: C 39 ASP cc_start: 0.8741 (p0) cc_final: 0.8456 (p0) REVERT: C 210 TYR cc_start: 0.8672 (m-80) cc_final: 0.8464 (m-80) REVERT: C 324 VAL cc_start: 0.8739 (t) cc_final: 0.8381 (m) REVERT: D 15 VAL cc_start: 0.6597 (t) cc_final: 0.6328 (t) REVERT: D 81 THR cc_start: 0.8396 (m) cc_final: 0.8169 (p) REVERT: D 86 MET cc_start: 0.6929 (ptp) cc_final: 0.6641 (ptp) REVERT: E 64 SER cc_start: 0.8284 (p) cc_final: 0.7602 (m) REVERT: H 8 VAL cc_start: 0.8996 (t) cc_final: 0.8633 (m) REVERT: L 5 MET cc_start: 0.8241 (tpp) cc_final: 0.7791 (tpp) REVERT: L 13 SER cc_start: 0.8372 (t) cc_final: 0.7979 (m) REVERT: M 21 LEU cc_start: 0.7775 (tp) cc_final: 0.7066 (tt) REVERT: M 83 TYR cc_start: 0.7792 (m-10) cc_final: 0.7574 (m-80) REVERT: N 6 THR cc_start: 0.8741 (t) cc_final: 0.8501 (p) outliers start: 38 outliers final: 30 residues processed: 196 average time/residue: 0.2174 time to fit residues: 66.3697 Evaluate side-chains 181 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13504 Z= 0.228 Angle : 0.613 9.205 18403 Z= 0.311 Chirality : 0.045 0.171 2089 Planarity : 0.005 0.059 2344 Dihedral : 6.288 87.822 1913 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.90 % Allowed : 18.00 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1681 helix: 1.87 (0.88), residues: 36 sheet: 0.24 (0.19), residues: 747 loop : -0.70 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 39 HIS 0.004 0.001 HIS A 211 PHE 0.031 0.002 PHE C 278 TYR 0.016 0.001 TYR H 98 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 1.308 Fit side-chains REVERT: A 39 ASP cc_start: 0.8485 (p0) cc_final: 0.8171 (p0) REVERT: B 88 PHE cc_start: 0.7183 (t80) cc_final: 0.6966 (t80) REVERT: B 296 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7526 (m-70) REVERT: C 39 ASP cc_start: 0.8775 (p0) cc_final: 0.8502 (p0) REVERT: C 210 TYR cc_start: 0.8711 (m-80) cc_final: 0.8382 (m-80) REVERT: C 324 VAL cc_start: 0.8730 (t) cc_final: 0.8325 (m) REVERT: D 8 VAL cc_start: 0.8835 (t) cc_final: 0.8463 (p) REVERT: D 14 LEU cc_start: 0.8317 (mt) cc_final: 0.8055 (mp) REVERT: D 15 VAL cc_start: 0.6664 (t) cc_final: 0.6419 (t) REVERT: D 81 THR cc_start: 0.8475 (m) cc_final: 0.8192 (p) REVERT: H 8 VAL cc_start: 0.8965 (t) cc_final: 0.8685 (m) REVERT: H 85 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6559 (tm-30) REVERT: L 5 MET cc_start: 0.8259 (tpp) cc_final: 0.7151 (tpp) REVERT: L 13 SER cc_start: 0.8406 (t) cc_final: 0.7962 (m) REVERT: M 21 LEU cc_start: 0.7590 (tp) cc_final: 0.7181 (tt) REVERT: M 83 TYR cc_start: 0.7848 (m-10) cc_final: 0.7623 (m-80) REVERT: N 6 THR cc_start: 0.8819 (t) cc_final: 0.8514 (p) REVERT: N 19 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7690 (ttt-90) REVERT: N 28 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7546 (tm-30) outliers start: 54 outliers final: 40 residues processed: 205 average time/residue: 0.2029 time to fit residues: 64.1285 Evaluate side-chains 188 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13504 Z= 0.246 Angle : 0.611 8.899 18403 Z= 0.310 Chirality : 0.045 0.164 2089 Planarity : 0.004 0.054 2344 Dihedral : 6.176 85.181 1913 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.99 % Allowed : 17.64 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1681 helix: 1.93 (0.87), residues: 36 sheet: 0.26 (0.19), residues: 736 loop : -0.69 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.036 0.002 PHE E 84 TYR 0.016 0.002 TYR N 92 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 1.477 Fit side-chains REVERT: A 39 ASP cc_start: 0.8492 (p0) cc_final: 0.8161 (p0) REVERT: A 278 PHE cc_start: 0.8696 (p90) cc_final: 0.8296 (p90) REVERT: B 88 PHE cc_start: 0.7028 (t80) cc_final: 0.6691 (t80) REVERT: B 296 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7707 (m-70) REVERT: C 39 ASP cc_start: 0.8688 (p0) cc_final: 0.8448 (p0) REVERT: C 210 TYR cc_start: 0.8707 (m-80) cc_final: 0.8339 (m-80) REVERT: D 8 VAL cc_start: 0.8827 (t) cc_final: 0.8443 (m) REVERT: D 14 LEU cc_start: 0.8397 (mt) cc_final: 0.8196 (mp) REVERT: D 15 VAL cc_start: 0.6760 (t) cc_final: 0.6549 (t) REVERT: D 79 LYS cc_start: 0.8369 (tptm) cc_final: 0.8112 (tptp) REVERT: D 81 THR cc_start: 0.8422 (m) cc_final: 0.8156 (p) REVERT: H 8 VAL cc_start: 0.8957 (t) cc_final: 0.8732 (m) REVERT: H 21 LEU cc_start: 0.7108 (tt) cc_final: 0.6785 (tt) REVERT: M 21 LEU cc_start: 0.7622 (tp) cc_final: 0.7186 (tt) REVERT: M 33 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7683 (m-10) REVERT: M 83 TYR cc_start: 0.7891 (m-10) cc_final: 0.7583 (m-80) REVERT: N 6 THR cc_start: 0.8902 (t) cc_final: 0.8609 (p) REVERT: N 19 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7735 (ttt-90) REVERT: N 28 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7486 (tm-30) outliers start: 69 outliers final: 53 residues processed: 221 average time/residue: 0.2191 time to fit residues: 73.9734 Evaluate side-chains 202 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 159 optimal weight: 0.0570 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 52 optimal weight: 0.3980 chunk 83 optimal weight: 0.0170 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13504 Z= 0.148 Angle : 0.576 8.614 18403 Z= 0.286 Chirality : 0.043 0.153 2089 Planarity : 0.004 0.053 2344 Dihedral : 5.875 84.420 1913 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.04 % Allowed : 20.46 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1681 helix: 2.36 (0.87), residues: 36 sheet: 0.54 (0.20), residues: 722 loop : -0.64 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 50 HIS 0.004 0.001 HIS A 211 PHE 0.034 0.001 PHE E 84 TYR 0.011 0.001 TYR N 94 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.638 Fit side-chains REVERT: A 39 ASP cc_start: 0.8434 (p0) cc_final: 0.8074 (p0) REVERT: A 49 LEU cc_start: 0.7170 (pt) cc_final: 0.6967 (pt) REVERT: A 278 PHE cc_start: 0.8472 (p90) cc_final: 0.8054 (p90) REVERT: B 88 PHE cc_start: 0.6910 (t80) cc_final: 0.6590 (t80) REVERT: B 296 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7652 (m-70) REVERT: B 319 LEU cc_start: 0.8101 (tp) cc_final: 0.7772 (mt) REVERT: C 39 ASP cc_start: 0.8784 (p0) cc_final: 0.8457 (p0) REVERT: C 210 TYR cc_start: 0.8660 (m-80) cc_final: 0.8267 (m-80) REVERT: D 8 VAL cc_start: 0.8839 (t) cc_final: 0.8508 (m) REVERT: D 14 LEU cc_start: 0.8357 (mt) cc_final: 0.8118 (mp) REVERT: D 79 LYS cc_start: 0.8262 (tptm) cc_final: 0.8032 (tptp) REVERT: D 81 THR cc_start: 0.8427 (m) cc_final: 0.8157 (p) REVERT: H 85 GLN cc_start: 0.7125 (tp-100) cc_final: 0.6481 (tm-30) REVERT: L 13 SER cc_start: 0.8378 (t) cc_final: 0.7962 (m) REVERT: M 83 TYR cc_start: 0.7773 (m-10) cc_final: 0.7555 (m-80) REVERT: N 6 THR cc_start: 0.8858 (t) cc_final: 0.8650 (p) REVERT: N 19 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7622 (ttt-90) REVERT: N 28 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7595 (tm-30) outliers start: 42 outliers final: 36 residues processed: 209 average time/residue: 0.1986 time to fit residues: 65.7364 Evaluate side-chains 190 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 159 optimal weight: 0.0050 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13504 Z= 0.190 Angle : 0.585 8.907 18403 Z= 0.292 Chirality : 0.043 0.167 2089 Planarity : 0.004 0.051 2344 Dihedral : 5.838 82.294 1913 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.12 % Allowed : 20.10 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1681 helix: 2.53 (0.87), residues: 36 sheet: 0.56 (0.20), residues: 721 loop : -0.68 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.036 0.001 PHE E 84 TYR 0.014 0.001 TYR H 98 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 1.650 Fit side-chains REVERT: A 39 ASP cc_start: 0.8425 (p0) cc_final: 0.8111 (p0) REVERT: A 278 PHE cc_start: 0.8551 (p90) cc_final: 0.8116 (p90) REVERT: B 88 PHE cc_start: 0.6827 (t80) cc_final: 0.6513 (t80) REVERT: B 296 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7699 (m-70) REVERT: B 319 LEU cc_start: 0.8125 (tp) cc_final: 0.7784 (mt) REVERT: C 39 ASP cc_start: 0.8698 (p0) cc_final: 0.8423 (p0) REVERT: C 210 TYR cc_start: 0.8669 (m-80) cc_final: 0.8361 (m-80) REVERT: D 8 VAL cc_start: 0.8839 (t) cc_final: 0.8474 (m) REVERT: D 81 THR cc_start: 0.8485 (m) cc_final: 0.8228 (p) REVERT: H 42 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7443 (tm-30) REVERT: H 80 ASN cc_start: 0.7560 (t0) cc_final: 0.7347 (t0) REVERT: L 13 SER cc_start: 0.8420 (t) cc_final: 0.8040 (m) REVERT: M 33 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7616 (m-10) REVERT: M 83 TYR cc_start: 0.7839 (m-10) cc_final: 0.7575 (m-80) REVERT: N 6 THR cc_start: 0.8858 (t) cc_final: 0.8638 (p) REVERT: N 19 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7812 (mtp-110) REVERT: N 28 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7699 (tm-30) outliers start: 57 outliers final: 46 residues processed: 205 average time/residue: 0.2068 time to fit residues: 66.1161 Evaluate side-chains 199 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13504 Z= 0.188 Angle : 0.586 9.008 18403 Z= 0.291 Chirality : 0.043 0.151 2089 Planarity : 0.004 0.051 2344 Dihedral : 5.783 79.965 1913 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.90 % Allowed : 20.90 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1681 helix: 2.74 (0.88), residues: 36 sheet: 0.59 (0.20), residues: 729 loop : -0.70 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.005 0.001 HIS C 211 PHE 0.046 0.001 PHE E 84 TYR 0.016 0.001 TYR N 94 ARG 0.005 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.623 Fit side-chains REVERT: A 39 ASP cc_start: 0.8451 (p0) cc_final: 0.8140 (p0) REVERT: A 278 PHE cc_start: 0.8537 (p90) cc_final: 0.8112 (p90) REVERT: B 88 PHE cc_start: 0.6804 (t80) cc_final: 0.6462 (t80) REVERT: B 273 TYR cc_start: 0.7242 (m-80) cc_final: 0.6895 (m-10) REVERT: B 319 LEU cc_start: 0.8175 (tp) cc_final: 0.7851 (mt) REVERT: C 39 ASP cc_start: 0.8696 (p0) cc_final: 0.8425 (p0) REVERT: C 210 TYR cc_start: 0.8661 (m-80) cc_final: 0.8283 (m-80) REVERT: C 273 TYR cc_start: 0.7512 (m-10) cc_final: 0.7276 (m-10) REVERT: D 8 VAL cc_start: 0.8817 (t) cc_final: 0.8500 (m) REVERT: D 81 THR cc_start: 0.8527 (m) cc_final: 0.8263 (p) REVERT: H 42 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7521 (tm-30) REVERT: H 80 ASN cc_start: 0.7680 (t0) cc_final: 0.7475 (t0) REVERT: L 13 SER cc_start: 0.8419 (t) cc_final: 0.8048 (m) REVERT: M 33 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7642 (m-10) REVERT: M 83 TYR cc_start: 0.7847 (m-10) cc_final: 0.7587 (m-80) REVERT: N 6 THR cc_start: 0.8844 (t) cc_final: 0.8622 (p) REVERT: N 19 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7773 (mtp-110) REVERT: N 28 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7775 (tm-30) outliers start: 54 outliers final: 49 residues processed: 201 average time/residue: 0.2089 time to fit residues: 65.4175 Evaluate side-chains 204 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13504 Z= 0.353 Angle : 0.658 9.468 18403 Z= 0.333 Chirality : 0.045 0.174 2089 Planarity : 0.005 0.051 2344 Dihedral : 6.081 74.483 1913 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.98 % Allowed : 20.82 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1681 helix: 2.66 (0.88), residues: 36 sheet: 0.34 (0.20), residues: 736 loop : -0.82 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 39 HIS 0.002 0.001 HIS C 211 PHE 0.044 0.002 PHE E 84 TYR 0.023 0.002 TYR N 92 ARG 0.006 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 1.572 Fit side-chains REVERT: A 39 ASP cc_start: 0.8521 (p0) cc_final: 0.8204 (p0) REVERT: A 278 PHE cc_start: 0.8729 (p90) cc_final: 0.8291 (p90) REVERT: B 88 PHE cc_start: 0.7013 (t80) cc_final: 0.6691 (t80) REVERT: C 39 ASP cc_start: 0.8722 (p0) cc_final: 0.8461 (p0) REVERT: C 210 TYR cc_start: 0.8725 (m-80) cc_final: 0.8408 (m-80) REVERT: C 273 TYR cc_start: 0.7675 (m-10) cc_final: 0.7336 (m-10) REVERT: D 8 VAL cc_start: 0.8913 (t) cc_final: 0.8583 (m) REVERT: D 81 THR cc_start: 0.8396 (m) cc_final: 0.8166 (p) REVERT: H 42 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7492 (tm-30) REVERT: L 5 MET cc_start: 0.7931 (tpp) cc_final: 0.7059 (tpp) REVERT: M 33 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: N 6 THR cc_start: 0.8907 (t) cc_final: 0.8637 (p) REVERT: N 28 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 55 outliers final: 45 residues processed: 203 average time/residue: 0.2028 time to fit residues: 63.9188 Evaluate side-chains 201 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 0.0870 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13504 Z= 0.206 Angle : 0.611 9.215 18403 Z= 0.307 Chirality : 0.044 0.160 2089 Planarity : 0.005 0.052 2344 Dihedral : 5.845 71.136 1913 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.40 % Allowed : 21.91 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1681 helix: 2.78 (0.88), residues: 36 sheet: 0.41 (0.20), residues: 724 loop : -0.74 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 50 HIS 0.004 0.001 HIS A 211 PHE 0.046 0.001 PHE E 84 TYR 0.018 0.001 TYR N 94 ARG 0.008 0.000 ARG L 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 1.532 Fit side-chains REVERT: A 39 ASP cc_start: 0.8496 (p0) cc_final: 0.8176 (p0) REVERT: A 278 PHE cc_start: 0.8601 (p90) cc_final: 0.8167 (p90) REVERT: B 88 PHE cc_start: 0.6889 (t80) cc_final: 0.6539 (t80) REVERT: C 39 ASP cc_start: 0.8688 (p0) cc_final: 0.8430 (p0) REVERT: C 210 TYR cc_start: 0.8672 (m-80) cc_final: 0.8346 (m-80) REVERT: C 273 TYR cc_start: 0.7643 (m-10) cc_final: 0.7320 (m-10) REVERT: D 8 VAL cc_start: 0.8886 (t) cc_final: 0.8561 (m) REVERT: D 81 THR cc_start: 0.8474 (m) cc_final: 0.8248 (p) REVERT: H 42 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7403 (tm-30) REVERT: L 5 MET cc_start: 0.7624 (tpp) cc_final: 0.6840 (tpp) REVERT: L 13 SER cc_start: 0.8484 (t) cc_final: 0.8032 (m) REVERT: M 33 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: N 6 THR cc_start: 0.8880 (t) cc_final: 0.8672 (p) REVERT: N 28 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7775 (tm-30) outliers start: 47 outliers final: 44 residues processed: 201 average time/residue: 0.2109 time to fit residues: 65.9971 Evaluate side-chains 201 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137105 restraints weight = 22060.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136654 restraints weight = 29224.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138307 restraints weight = 26275.565| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13504 Z= 0.244 Angle : 0.622 9.385 18403 Z= 0.312 Chirality : 0.044 0.158 2089 Planarity : 0.005 0.051 2344 Dihedral : 5.850 68.206 1913 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.98 % Allowed : 21.26 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1681 helix: 2.71 (0.88), residues: 36 sheet: 0.39 (0.20), residues: 718 loop : -0.72 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 39 HIS 0.004 0.001 HIS C 211 PHE 0.044 0.002 PHE C 278 TYR 0.017 0.001 TYR N 92 ARG 0.008 0.000 ARG M 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2556.53 seconds wall clock time: 48 minutes 2.52 seconds (2882.52 seconds total)