Starting phenix.real_space_refine on Fri Jan 24 06:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpl_27637/01_2025/8dpl_27637.cif" } resolution = 2.53 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= -0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5541 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 10665 2.51 5 N 2835 2.21 5 O 3309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16872 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "J" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "M" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1344 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.72, per 1000 atoms: 0.52 Number of scatterers: 16872 At special positions: 0 Unit cell: (129.69, 127.71, 121.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3309 8.00 N 2835 7.00 C 10665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 161 " - pdb=" SG CYS O 226 " distance=2.03 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 121 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 511 " - pdb=" SG CYS J 556 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS M 108 " - pdb=" SG CYS M 135 " distance=2.03 Simple disulfide: pdb=" SG CYS M 121 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS N 511 " - pdb=" SG CYS N 556 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG D 401 " - " ASN D 228 " " NAG I 401 " - " ASN I 228 " " NAG M 401 " - " ASN M 228 " " NAG P 1 " - " ASN J 563 " " NAG Q 1 " - " ASN E 563 " " NAG R 1 " - " ASN N 563 " Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 9.8% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.600A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.999A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.588A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.006A pdb=" N SER C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.588A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.993A pdb=" N SER O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 74 Processing helix chain 'I' and resid 78 through 84 removed outlier: 3.658A pdb=" N LYS I 84 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 541 Processing helix chain 'J' and resid 551 through 576 removed outlier: 3.670A pdb=" N ILE J 555 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR J 566 " --> pdb=" O ALA J 562 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN J 567 " --> pdb=" O ASN J 563 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA J 568 " --> pdb=" O GLU J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 597 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.696A pdb=" N LYS D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 551 through 576 removed outlier: 3.667A pdb=" N ILE E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'M' and resid 71 through 74 Processing helix chain 'M' and resid 78 through 84 removed outlier: 3.667A pdb=" N LYS M 84 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 541 Processing helix chain 'N' and resid 551 through 576 removed outlier: 3.680A pdb=" N ILE N 555 " --> pdb=" O GLN N 551 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR N 566 " --> pdb=" O ALA N 562 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN N 567 " --> pdb=" O ASN N 563 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA N 568 " --> pdb=" O GLU N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 583 through 597 Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.727A pdb=" N TYR F 102 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP F 107 " --> pdb=" O TYR F 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.718A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.627A pdb=" N VAL H 157 " --> pdb=" O ILE H 213 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR H 207 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N GLN H 165 " --> pdb=" O SER H 205 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER H 205 " --> pdb=" O GLN H 165 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N VAL H 167 " --> pdb=" O SER H 203 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N SER H 203 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 191 through 192 removed outlier: 5.268A pdb=" N LEU H 184 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN H 175 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 186 " --> pdb=" O TRP H 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.895A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.747A pdb=" N TYR A 102 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP A 107 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.748A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.876A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.876A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.620A pdb=" N VAL C 157 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR C 207 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N GLN C 165 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N SER C 205 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N VAL C 167 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N SER C 203 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.634A pdb=" N TRP C 173 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR C 187 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 171 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.887A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.742A pdb=" N TYR K 102 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP K 107 " --> pdb=" O TYR K 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.731A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AD1, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.874A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR O 107 " --> pdb=" O ARG O 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.874A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 142 through 144 removed outlier: 3.623A pdb=" N VAL O 157 " --> pdb=" O ILE O 213 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR O 207 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N GLN O 165 " --> pdb=" O SER O 205 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N SER O 205 " --> pdb=" O GLN O 165 " (cutoff:3.500A) removed outlier: 12.168A pdb=" N VAL O 167 " --> pdb=" O SER O 203 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N SER O 203 " --> pdb=" O VAL O 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 191 through 192 removed outlier: 5.263A pdb=" N LEU O 184 " --> pdb=" O GLN O 175 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN O 175 " --> pdb=" O LEU O 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE O 186 " --> pdb=" O TRP O 173 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 42 through 45 removed outlier: 3.927A pdb=" N ILE I 38 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 42 through 45 removed outlier: 3.927A pdb=" N ILE I 38 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL I 96 " --> pdb=" O THR J 581 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AE1, first strand: chain 'I' and resid 102 through 103 removed outlier: 3.540A pdb=" N LEU J 515 " --> pdb=" O MET J 548 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 108 through 114 removed outlier: 6.645A pdb=" N CYS I 108 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL I 141 " --> pdb=" O CYS I 108 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN I 110 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY I 143 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU I 112 " --> pdb=" O GLY I 143 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.920A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.920A pdb=" N ILE D 38 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AE6, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.534A pdb=" N LEU E 515 " --> pdb=" O MET E 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 108 through 114 removed outlier: 6.648A pdb=" N CYS D 108 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 141 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN D 110 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY D 143 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU D 112 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 42 through 45 removed outlier: 3.917A pdb=" N ILE M 38 " --> pdb=" O ILE M 185 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 42 through 45 removed outlier: 3.917A pdb=" N ILE M 38 " --> pdb=" O ILE M 185 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL M 96 " --> pdb=" O THR N 581 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 86 through 89 Processing sheet with id=AF2, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.536A pdb=" N LEU N 515 " --> pdb=" O MET N 548 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 108 through 114 removed outlier: 6.641A pdb=" N CYS M 108 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL M 141 " --> pdb=" O CYS M 108 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN M 110 " --> pdb=" O VAL M 141 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY M 143 " --> pdb=" O ASN M 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU M 112 " --> pdb=" O GLY M 143 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1623 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: 6.04 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5358 1.34 - 1.46: 4264 1.46 - 1.58: 7568 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 17271 Sorted by residual: bond pdb=" C1 MAN P 6 " pdb=" C2 MAN P 6 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN R 6 " pdb=" C2 MAN R 6 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 MAN Q 6 " pdb=" C2 MAN Q 6 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 17266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 22897 1.28 - 2.55: 406 2.55 - 3.83: 104 3.83 - 5.10: 41 5.10 - 6.38: 15 Bond angle restraints: 23463 Sorted by residual: angle pdb=" C TYR O 230 " pdb=" N SER O 231 " pdb=" CA SER O 231 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.41e+00 angle pdb=" N SER C 231 " pdb=" CA SER C 231 " pdb=" CB SER C 231 " ideal model delta sigma weight residual 113.65 110.07 3.58 1.47e+00 4.63e-01 5.92e+00 angle pdb=" N SER H 231 " pdb=" CA SER H 231 " pdb=" CB SER H 231 " ideal model delta sigma weight residual 113.65 110.14 3.51 1.47e+00 4.63e-01 5.71e+00 angle pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" O2 MAN R 4 " ideal model delta sigma weight residual 111.77 105.39 6.38 3.00e+00 1.11e-01 4.52e+00 angle pdb=" C3 MAN P 4 " pdb=" C2 MAN P 4 " pdb=" O2 MAN P 4 " ideal model delta sigma weight residual 111.77 105.40 6.37 3.00e+00 1.11e-01 4.50e+00 ... (remaining 23458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 10122 21.63 - 43.26: 177 43.26 - 64.89: 12 64.89 - 86.52: 18 86.52 - 108.16: 12 Dihedral angle restraints: 10341 sinusoidal: 4209 harmonic: 6132 Sorted by residual: dihedral pdb=" CA TYR K 104 " pdb=" C TYR K 104 " pdb=" N ASN K 105 " pdb=" CA ASN K 105 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR F 104 " pdb=" C TYR F 104 " pdb=" N ASN F 105 " pdb=" CA ASN F 105 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR A 104 " pdb=" C TYR A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 10338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2460 0.099 - 0.199: 162 0.199 - 0.298: 3 0.298 - 0.397: 0 0.397 - 0.496: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN J 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN N 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 2625 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 234 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO H 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO O 233 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO O 234 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO O 234 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO O 234 " 0.028 5.00e-02 4.00e+02 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4121 2.80 - 3.33: 14026 3.33 - 3.85: 27142 3.85 - 4.38: 33011 4.38 - 4.90: 57882 Nonbonded interactions: 136182 Sorted by model distance: nonbonded pdb=" OE1 GLN H 144 " pdb=" OG1 THR H 241 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN C 144 " pdb=" OG1 THR C 241 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN O 144 " pdb=" OG1 THR O 241 " model vdw 2.285 3.040 nonbonded pdb=" O7 NAG P 2 " pdb=" O4 MAN P 4 " model vdw 2.286 3.040 nonbonded pdb=" O7 NAG R 2 " pdb=" O4 MAN R 4 " model vdw 2.287 3.040 ... (remaining 136177 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: 0.11 Found NCS groups: ncs_group { reference = chain 'Q' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 38.130 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.100 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.002 0.031 17271 Z= 0.144 Angle : 0.482 6.377 23463 Z= 0.250 Chirality : 0.045 0.496 2628 Planarity : 0.003 0.050 2967 Dihedral : 9.406 108.156 6396 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2115 helix: 1.16 (0.39), residues: 174 sheet: 1.27 (0.18), residues: 906 loop : 0.28 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 47 HIS 0.003 0.001 HIS H 229 PHE 0.005 0.001 PHE M 225 TYR 0.010 0.001 TYR K 106 ARG 0.002 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.8179 (t) cc_final: 0.7914 (t) REVERT: F 106 TYR cc_start: 0.6880 (m-80) cc_final: 0.6559 (m-80) REVERT: K 100 THR cc_start: 0.8034 (t) cc_final: 0.7762 (t) REVERT: L 87 ASP cc_start: 0.8217 (m-30) cc_final: 0.7727 (m-30) REVERT: D 228 ASN cc_start: 0.8380 (p0) cc_final: 0.8048 (p0) outliers start: 0 outliers final: 6 residues processed: 507 average time/residue: 1.5356 time to fit residues: 853.5129 Evaluate side-chains 340 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain O residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 31 ASN C 6 GLN L 28 ASN I 44 GLN D 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045655 restraints weight = 45726.239| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.53 r_work: 0.2557 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 17271 Z= 0.438 Angle : 0.658 7.891 23463 Z= 0.337 Chirality : 0.046 0.168 2628 Planarity : 0.005 0.051 2967 Dihedral : 8.809 96.455 2775 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.14 % Allowed : 14.13 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2115 helix: 2.00 (0.39), residues: 156 sheet: 0.92 (0.17), residues: 918 loop : 0.23 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 47 HIS 0.007 0.001 HIS H 229 PHE 0.019 0.001 PHE A 97 TYR 0.016 0.002 TYR A 104 ARG 0.008 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 346 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8320 (tt0) cc_final: 0.8097 (tt0) REVERT: F 75 ASP cc_start: 0.8459 (t0) cc_final: 0.7952 (t0) REVERT: F 103 ARG cc_start: 0.9007 (mtp-110) cc_final: 0.8205 (ttp80) REVERT: G 17 ARG cc_start: 0.9136 (mtp-110) cc_final: 0.8509 (ttp80) REVERT: G 85 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8194 (mm-30) REVERT: H 40 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8521 (mmm160) REVERT: H 46 GLU cc_start: 0.8238 (mp0) cc_final: 0.7810 (mp0) REVERT: H 59 ASP cc_start: 0.8659 (t0) cc_final: 0.8259 (t0) REVERT: H 73 ASP cc_start: 0.8568 (t0) cc_final: 0.8347 (t0) REVERT: H 220 ASP cc_start: 0.9004 (m-30) cc_final: 0.8776 (m-30) REVERT: A 103 ARG cc_start: 0.8954 (mtp-110) cc_final: 0.8059 (ttp80) REVERT: B 85 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8140 (mm-30) REVERT: C 40 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8428 (mmm160) REVERT: C 46 GLU cc_start: 0.8367 (mp0) cc_final: 0.7982 (mp0) REVERT: C 59 ASP cc_start: 0.8758 (t0) cc_final: 0.8502 (t0) REVERT: C 220 ASP cc_start: 0.9111 (m-30) cc_final: 0.8796 (m-30) REVERT: C 221 MET cc_start: 0.6563 (mmt) cc_final: 0.5834 (mmt) REVERT: K 46 GLU cc_start: 0.8611 (tt0) cc_final: 0.8109 (tt0) REVERT: K 103 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8574 (ptm160) REVERT: K 107 ASP cc_start: 0.8860 (m-30) cc_final: 0.8502 (m-30) REVERT: L 85 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8025 (mm-30) REVERT: L 94 ASP cc_start: 0.8004 (t0) cc_final: 0.7769 (t70) REVERT: O 40 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8533 (mmm160) REVERT: O 46 GLU cc_start: 0.8373 (mp0) cc_final: 0.7870 (mp0) REVERT: O 73 ASP cc_start: 0.8704 (t0) cc_final: 0.8484 (t0) REVERT: I 100 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8707 (mt-10) REVERT: I 112 GLU cc_start: 0.8006 (mp0) cc_final: 0.7798 (mp0) REVERT: J 523 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: J 595 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8655 (tt0) REVERT: D 112 GLU cc_start: 0.7998 (mp0) cc_final: 0.7764 (mp0) REVERT: D 228 ASN cc_start: 0.8188 (p0) cc_final: 0.7954 (p0) REVERT: E 523 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: M 112 GLU cc_start: 0.8123 (mp0) cc_final: 0.7891 (mp0) REVERT: M 136 ARG cc_start: 0.8511 (tpt90) cc_final: 0.7078 (tpm170) REVERT: M 178 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9053 (mt-10) REVERT: M 231 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7480 (mt-10) REVERT: N 540 GLU cc_start: 0.9106 (mp0) cc_final: 0.8885 (pm20) REVERT: N 595 GLN cc_start: 0.8969 (tp40) cc_final: 0.8551 (tt0) outliers start: 38 outliers final: 20 residues processed: 362 average time/residue: 1.6263 time to fit residues: 642.2534 Evaluate side-chains 335 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 576 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 175 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 105 ASN G 28 ASN H 6 GLN A 31 ASN A 105 ASN O 6 GLN I 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.047313 restraints weight = 45219.661| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.52 r_work: 0.2588 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17271 Z= 0.172 Angle : 0.604 8.553 23463 Z= 0.303 Chirality : 0.043 0.172 2628 Planarity : 0.004 0.054 2967 Dihedral : 7.900 72.517 2765 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.75 % Allowed : 14.58 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2115 helix: 2.37 (0.40), residues: 156 sheet: 0.92 (0.17), residues: 924 loop : 0.13 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.004 0.001 HIS H 229 PHE 0.014 0.001 PHE H 148 TYR 0.014 0.001 TYR B 51 ARG 0.009 0.001 ARG J 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 362 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8898 (mmmm) REVERT: F 46 GLU cc_start: 0.8314 (tt0) cc_final: 0.8016 (tt0) REVERT: F 75 ASP cc_start: 0.8439 (t0) cc_final: 0.8020 (t0) REVERT: F 92 ASP cc_start: 0.9201 (m-30) cc_final: 0.8612 (m-30) REVERT: F 103 ARG cc_start: 0.9050 (mtp-110) cc_final: 0.8720 (ttp80) REVERT: F 105 ASN cc_start: 0.8963 (m110) cc_final: 0.8647 (m-40) REVERT: G 85 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8136 (mm-30) REVERT: G 98 ARG cc_start: 0.8793 (mpp80) cc_final: 0.8345 (mmp80) REVERT: H 40 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8499 (mmm160) REVERT: H 46 GLU cc_start: 0.8303 (mp0) cc_final: 0.7882 (mp0) REVERT: H 59 ASP cc_start: 0.8668 (t0) cc_final: 0.8247 (t0) REVERT: H 220 ASP cc_start: 0.9187 (m-30) cc_final: 0.8823 (m-30) REVERT: A 43 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8948 (mmmm) REVERT: A 103 ARG cc_start: 0.8939 (mtp-110) cc_final: 0.8534 (ttp80) REVERT: A 105 ASN cc_start: 0.9023 (m110) cc_final: 0.8673 (m-40) REVERT: B 85 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 109 LEU cc_start: 0.8788 (tp) cc_final: 0.8411 (tm) REVERT: C 40 ARG cc_start: 0.8703 (mmm160) cc_final: 0.8418 (mmm160) REVERT: C 46 GLU cc_start: 0.8421 (mp0) cc_final: 0.7927 (mp0) REVERT: C 220 ASP cc_start: 0.9238 (m-30) cc_final: 0.8796 (m-30) REVERT: C 221 MET cc_start: 0.6272 (mmt) cc_final: 0.5514 (mmt) REVERT: K 43 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8857 (mmmm) REVERT: K 46 GLU cc_start: 0.8601 (tt0) cc_final: 0.8121 (tt0) REVERT: K 92 ASP cc_start: 0.9139 (m-30) cc_final: 0.8580 (m-30) REVERT: K 103 ARG cc_start: 0.9109 (mtp-110) cc_final: 0.8512 (ptm160) REVERT: K 107 ASP cc_start: 0.8838 (m-30) cc_final: 0.8331 (m-30) REVERT: L 85 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8132 (mm-30) REVERT: L 98 ARG cc_start: 0.8901 (mpp80) cc_final: 0.8502 (mmp80) REVERT: O 40 ARG cc_start: 0.8818 (mmm160) cc_final: 0.8527 (mmm160) REVERT: O 46 GLU cc_start: 0.8386 (mp0) cc_final: 0.7936 (mp0) REVERT: I 100 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8689 (mt-10) REVERT: I 112 GLU cc_start: 0.8075 (mp0) cc_final: 0.7775 (mp0) REVERT: I 228 ASN cc_start: 0.8686 (p0) cc_final: 0.8421 (p0) REVERT: I 231 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7234 (mt-10) REVERT: J 544 THR cc_start: 0.9380 (m) cc_final: 0.9093 (p) REVERT: J 595 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8575 (tt0) REVERT: D 112 GLU cc_start: 0.8049 (mp0) cc_final: 0.7764 (mp0) REVERT: D 136 ARG cc_start: 0.8691 (tpm-80) cc_final: 0.7482 (tpm170) REVERT: D 228 ASN cc_start: 0.8287 (p0) cc_final: 0.8068 (p0) REVERT: E 523 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: M 100 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8559 (pt0) REVERT: M 106 GLU cc_start: 0.8725 (tp30) cc_final: 0.8431 (tp30) REVERT: M 112 GLU cc_start: 0.8205 (mp0) cc_final: 0.7892 (mp0) REVERT: M 136 ARG cc_start: 0.8434 (tpt90) cc_final: 0.7305 (tpm170) REVERT: M 178 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8918 (mt-10) REVERT: M 231 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7057 (mt-10) REVERT: N 523 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: N 540 GLU cc_start: 0.9125 (mp0) cc_final: 0.8911 (pm20) outliers start: 31 outliers final: 13 residues processed: 373 average time/residue: 1.5866 time to fit residues: 646.1089 Evaluate side-chains 348 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 152 optimal weight: 0.0570 chunk 182 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.046032 restraints weight = 45729.978| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.50 r_work: 0.2561 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17271 Z= 0.281 Angle : 0.621 7.914 23463 Z= 0.313 Chirality : 0.044 0.173 2628 Planarity : 0.005 0.061 2967 Dihedral : 7.914 72.334 2763 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.14 % Allowed : 14.98 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2115 helix: 2.51 (0.40), residues: 156 sheet: 0.79 (0.17), residues: 912 loop : 0.00 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.006 0.001 HIS H 229 PHE 0.012 0.001 PHE A 97 TYR 0.023 0.001 TYR G 51 ARG 0.010 0.001 ARG J 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8443 (tt0) cc_final: 0.8035 (tt0) REVERT: F 75 ASP cc_start: 0.8490 (t0) cc_final: 0.8005 (t0) REVERT: F 92 ASP cc_start: 0.9249 (m-30) cc_final: 0.8740 (m-30) REVERT: G 85 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8090 (mm-30) REVERT: G 98 ARG cc_start: 0.8915 (mpp80) cc_final: 0.8391 (mmp80) REVERT: H 46 GLU cc_start: 0.8386 (mp0) cc_final: 0.7943 (mp0) REVERT: H 59 ASP cc_start: 0.8725 (t0) cc_final: 0.8285 (t0) REVERT: H 220 ASP cc_start: 0.9156 (m-30) cc_final: 0.8788 (m-30) REVERT: A 89 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8227 (mmtt) REVERT: A 92 ASP cc_start: 0.9187 (m-30) cc_final: 0.8653 (m-30) REVERT: A 103 ARG cc_start: 0.8928 (mtp-110) cc_final: 0.8519 (ttp80) REVERT: A 105 ASN cc_start: 0.8985 (m110) cc_final: 0.8512 (m-40) REVERT: B 85 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8341 (mm-30) REVERT: C 46 GLU cc_start: 0.8500 (mp0) cc_final: 0.8112 (mp0) REVERT: C 59 ASP cc_start: 0.8760 (t0) cc_final: 0.8467 (t0) REVERT: C 220 ASP cc_start: 0.9221 (m-30) cc_final: 0.8772 (m-30) REVERT: C 221 MET cc_start: 0.6298 (mmt) cc_final: 0.5501 (mmt) REVERT: K 46 GLU cc_start: 0.8611 (tt0) cc_final: 0.8138 (tt0) REVERT: K 92 ASP cc_start: 0.9148 (m-30) cc_final: 0.8709 (m-30) REVERT: K 103 ARG cc_start: 0.9130 (mtp-110) cc_final: 0.8539 (ptm160) REVERT: K 107 ASP cc_start: 0.8862 (m-30) cc_final: 0.8303 (m-30) REVERT: L 85 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8194 (mm-30) REVERT: O 46 GLU cc_start: 0.8440 (mp0) cc_final: 0.7913 (mp0) REVERT: I 100 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8741 (mt-10) REVERT: I 112 GLU cc_start: 0.8073 (mp0) cc_final: 0.7729 (mp0) REVERT: I 228 ASN cc_start: 0.8749 (p0) cc_final: 0.8467 (p0) REVERT: J 523 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: J 544 THR cc_start: 0.9394 (m) cc_final: 0.9080 (p) REVERT: D 56 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8656 (mmmt) REVERT: D 112 GLU cc_start: 0.8064 (mp0) cc_final: 0.7752 (mp0) REVERT: D 136 ARG cc_start: 0.8529 (tpm-80) cc_final: 0.7350 (tpm170) REVERT: D 228 ASN cc_start: 0.8419 (p0) cc_final: 0.8158 (p0) REVERT: E 523 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6999 (pt0) REVERT: M 106 GLU cc_start: 0.8743 (tp30) cc_final: 0.8476 (tp30) REVERT: M 112 GLU cc_start: 0.8221 (mp0) cc_final: 0.7876 (mp0) REVERT: M 178 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9053 (mt-10) REVERT: M 214 TYR cc_start: 0.7907 (p90) cc_final: 0.7547 (p90) REVERT: N 523 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: N 540 GLU cc_start: 0.9138 (mp0) cc_final: 0.8908 (pm20) REVERT: N 595 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8561 (tt0) outliers start: 38 outliers final: 20 residues processed: 360 average time/residue: 1.5911 time to fit residues: 625.9719 Evaluate side-chains 353 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 329 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 576 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 153 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.042913 restraints weight = 46629.879| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.53 r_work: 0.2485 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 17271 Z= 0.569 Angle : 0.721 8.111 23463 Z= 0.368 Chirality : 0.047 0.208 2628 Planarity : 0.005 0.067 2967 Dihedral : 8.378 76.382 2763 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.36 % Allowed : 16.05 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2115 helix: 2.38 (0.41), residues: 156 sheet: 0.63 (0.17), residues: 915 loop : -0.31 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 47 HIS 0.009 0.002 HIS H 229 PHE 0.018 0.002 PHE A 97 TYR 0.037 0.002 TYR F 106 ARG 0.011 0.001 ARG J 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 327 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8874 (mmmm) REVERT: F 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8227 (tt0) REVERT: F 75 ASP cc_start: 0.8576 (t0) cc_final: 0.7954 (t0) REVERT: F 92 ASP cc_start: 0.9259 (m-30) cc_final: 0.8793 (m-30) REVERT: G 85 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8056 (mm-30) REVERT: G 98 ARG cc_start: 0.9117 (mpp80) cc_final: 0.8915 (mpp80) REVERT: H 46 GLU cc_start: 0.8426 (mp0) cc_final: 0.8090 (mp0) REVERT: H 59 ASP cc_start: 0.8852 (t0) cc_final: 0.8308 (t0) REVERT: H 220 ASP cc_start: 0.9147 (m-30) cc_final: 0.8810 (m-30) REVERT: A 89 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8206 (mmtt) REVERT: A 92 ASP cc_start: 0.9219 (m-30) cc_final: 0.8737 (m-30) REVERT: A 105 ASN cc_start: 0.9047 (m110) cc_final: 0.8744 (p0) REVERT: B 85 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8314 (mm-30) REVERT: B 98 ARG cc_start: 0.9073 (mpp80) cc_final: 0.8617 (mmp80) REVERT: C 46 GLU cc_start: 0.8570 (mp0) cc_final: 0.8127 (mp0) REVERT: C 220 ASP cc_start: 0.9176 (m-30) cc_final: 0.8712 (m-30) REVERT: C 221 MET cc_start: 0.6372 (mmt) cc_final: 0.5548 (mmt) REVERT: K 43 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8836 (mmmm) REVERT: K 46 GLU cc_start: 0.8618 (tt0) cc_final: 0.8158 (tt0) REVERT: K 61 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (p0) REVERT: K 89 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7877 (mmtt) REVERT: K 92 ASP cc_start: 0.9270 (m-30) cc_final: 0.8846 (m-30) REVERT: K 105 ASN cc_start: 0.8597 (t0) cc_final: 0.8379 (t0) REVERT: K 107 ASP cc_start: 0.8954 (m-30) cc_final: 0.8719 (m-30) REVERT: L 85 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8336 (mm-30) REVERT: O 46 GLU cc_start: 0.8477 (mp0) cc_final: 0.8018 (mp0) REVERT: I 100 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8702 (mt-10) REVERT: I 112 GLU cc_start: 0.8181 (mp0) cc_final: 0.7844 (mp0) REVERT: I 156 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8845 (mm-30) REVERT: J 523 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: J 595 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8799 (tt0) REVERT: D 56 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8719 (mmmt) REVERT: D 106 GLU cc_start: 0.8885 (tp30) cc_final: 0.8657 (tp30) REVERT: D 112 GLU cc_start: 0.8148 (mp0) cc_final: 0.7782 (mp0) REVERT: D 231 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7068 (mt-10) REVERT: E 523 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6803 (pt0) REVERT: M 100 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8690 (pt0) REVERT: M 106 GLU cc_start: 0.8887 (tp30) cc_final: 0.8560 (tp30) REVERT: M 112 GLU cc_start: 0.8279 (mp0) cc_final: 0.7919 (mp0) REVERT: N 523 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7256 (pt0) outliers start: 42 outliers final: 23 residues processed: 347 average time/residue: 1.6000 time to fit residues: 605.9914 Evaluate side-chains 334 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 306 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 156 GLU Chi-restraints excluded: chain I residue 178 GLU Chi-restraints excluded: chain J residue 523 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN A 112 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.045610 restraints weight = 45659.011| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.50 r_work: 0.2548 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17271 Z= 0.203 Angle : 0.655 8.627 23463 Z= 0.330 Chirality : 0.044 0.170 2628 Planarity : 0.005 0.060 2967 Dihedral : 7.695 67.832 2763 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.25 % Allowed : 17.57 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2115 helix: 2.54 (0.41), residues: 156 sheet: 0.72 (0.17), residues: 912 loop : -0.28 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.005 0.001 HIS H 229 PHE 0.010 0.001 PHE K 97 TYR 0.027 0.001 TYR G 51 ARG 0.012 0.001 ARG E 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 342 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8477 (tt0) cc_final: 0.8138 (tt0) REVERT: F 75 ASP cc_start: 0.8571 (t0) cc_final: 0.8125 (t0) REVERT: F 89 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7787 (mmtt) REVERT: F 92 ASP cc_start: 0.9241 (m-30) cc_final: 0.8772 (m-30) REVERT: G 17 ARG cc_start: 0.9158 (mtp-110) cc_final: 0.8930 (mmm160) REVERT: G 85 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8165 (mm-30) REVERT: G 98 ARG cc_start: 0.8912 (mpp80) cc_final: 0.8515 (mmp80) REVERT: H 46 GLU cc_start: 0.8463 (mp0) cc_final: 0.8102 (mp0) REVERT: H 59 ASP cc_start: 0.8804 (t0) cc_final: 0.8254 (t0) REVERT: H 220 ASP cc_start: 0.9132 (m-30) cc_final: 0.8802 (m-30) REVERT: A 43 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8778 (mmmm) REVERT: A 51 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9419 (tp) REVERT: A 75 ASP cc_start: 0.8622 (t0) cc_final: 0.7804 (t0) REVERT: A 78 LYS cc_start: 0.9528 (ptpp) cc_final: 0.9279 (ptpp) REVERT: A 89 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8226 (mmtt) REVERT: A 92 ASP cc_start: 0.9229 (m-30) cc_final: 0.8736 (m-30) REVERT: A 103 ARG cc_start: 0.8966 (mtp-110) cc_final: 0.8527 (ttp80) REVERT: A 105 ASN cc_start: 0.9048 (m110) cc_final: 0.8622 (m-40) REVERT: B 85 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8454 (mm-30) REVERT: B 98 ARG cc_start: 0.8920 (mpp80) cc_final: 0.8577 (mmp80) REVERT: C 46 GLU cc_start: 0.8583 (mp0) cc_final: 0.8206 (mp0) REVERT: C 59 ASP cc_start: 0.8724 (t0) cc_final: 0.8448 (t0) REVERT: C 220 ASP cc_start: 0.9173 (m-30) cc_final: 0.8729 (m-30) REVERT: C 221 MET cc_start: 0.6288 (mmt) cc_final: 0.5499 (mmt) REVERT: K 43 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8803 (mmmm) REVERT: K 46 GLU cc_start: 0.8590 (tt0) cc_final: 0.8141 (tt0) REVERT: K 75 ASP cc_start: 0.8590 (t0) cc_final: 0.8107 (t0) REVERT: K 92 ASP cc_start: 0.9269 (m-30) cc_final: 0.8791 (m-30) REVERT: K 103 ARG cc_start: 0.9098 (mtp-110) cc_final: 0.8079 (ttp-110) REVERT: K 105 ASN cc_start: 0.8600 (t0) cc_final: 0.8369 (m110) REVERT: L 85 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8313 (mm-30) REVERT: O 46 GLU cc_start: 0.8461 (mp0) cc_final: 0.7952 (mp0) REVERT: O 156 ARG cc_start: 0.9414 (mtp-110) cc_final: 0.9136 (ttm110) REVERT: I 100 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8695 (mt-10) REVERT: I 112 GLU cc_start: 0.8138 (mp0) cc_final: 0.7828 (mp0) REVERT: J 544 THR cc_start: 0.9405 (m) cc_final: 0.9071 (p) REVERT: J 595 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8695 (tt0) REVERT: D 56 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8711 (mmmt) REVERT: D 106 GLU cc_start: 0.8896 (tp30) cc_final: 0.8605 (tp30) REVERT: D 112 GLU cc_start: 0.8113 (mp0) cc_final: 0.7780 (mp0) REVERT: D 136 ARG cc_start: 0.8415 (tpm-80) cc_final: 0.7231 (tpm170) REVERT: D 156 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8930 (mm-30) REVERT: E 523 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: M 100 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8675 (pt0) REVERT: M 106 GLU cc_start: 0.8889 (tp30) cc_final: 0.8626 (tp30) REVERT: M 112 GLU cc_start: 0.8253 (mp0) cc_final: 0.7916 (mp0) REVERT: N 523 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: N 595 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8601 (tt0) outliers start: 40 outliers final: 24 residues processed: 363 average time/residue: 1.5791 time to fit residues: 628.8054 Evaluate side-chains 351 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 597 TRP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 204 optimal weight: 0.4980 chunk 201 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 16 optimal weight: 0.0050 chunk 69 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.7156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.044398 restraints weight = 45714.815| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.53 r_work: 0.2532 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17271 Z= 0.292 Angle : 0.676 9.082 23463 Z= 0.341 Chirality : 0.044 0.171 2628 Planarity : 0.005 0.063 2967 Dihedral : 7.762 68.932 2763 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.25 % Allowed : 18.07 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2115 helix: 2.63 (0.41), residues: 156 sheet: 0.71 (0.17), residues: 906 loop : -0.31 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS O 229 PHE 0.014 0.001 PHE H 148 TYR 0.031 0.001 TYR F 106 ARG 0.013 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4230 Ramachandran restraints generated. 2115 Oldfield, 0 Emsley, 2115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8155 (tt0) REVERT: F 54 LYS cc_start: 0.9546 (tppp) cc_final: 0.9340 (tppt) REVERT: F 75 ASP cc_start: 0.8600 (t0) cc_final: 0.7524 (t0) REVERT: F 92 ASP cc_start: 0.9252 (m-30) cc_final: 0.8812 (m-30) REVERT: G 85 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8143 (mm-30) REVERT: G 98 ARG cc_start: 0.8973 (mpp80) cc_final: 0.8553 (mmp80) REVERT: H 46 GLU cc_start: 0.8476 (mp0) cc_final: 0.8040 (mp0) REVERT: H 59 ASP cc_start: 0.8819 (t0) cc_final: 0.8281 (t0) REVERT: H 220 ASP cc_start: 0.9131 (m-30) cc_final: 0.8801 (m-30) REVERT: A 43 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8725 (mmmm) REVERT: A 51 ILE cc_start: 0.9652 (OUTLIER) cc_final: 0.9430 (tp) REVERT: A 75 ASP cc_start: 0.8642 (t0) cc_final: 0.8162 (t0) REVERT: A 89 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8194 (mmtp) REVERT: A 92 ASP cc_start: 0.9219 (m-30) cc_final: 0.8703 (m-30) REVERT: A 105 ASN cc_start: 0.9046 (m110) cc_final: 0.8705 (p0) REVERT: B 85 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8477 (mm-30) REVERT: C 10 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8514 (mm-30) REVERT: C 46 GLU cc_start: 0.8626 (mp0) cc_final: 0.8268 (mp0) REVERT: C 59 ASP cc_start: 0.8755 (t0) cc_final: 0.8539 (t0) REVERT: C 156 ARG cc_start: 0.9433 (mtp-110) cc_final: 0.9223 (ttm110) REVERT: C 220 ASP cc_start: 0.9172 (m-30) cc_final: 0.8721 (m-30) REVERT: C 221 MET cc_start: 0.6372 (mmt) cc_final: 0.5551 (mmt) REVERT: K 43 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8783 (mmmm) REVERT: K 46 GLU cc_start: 0.8590 (tt0) cc_final: 0.8143 (tt0) REVERT: K 61 ASP cc_start: 0.8580 (p0) cc_final: 0.8112 (p0) REVERT: K 75 ASP cc_start: 0.8628 (t0) cc_final: 0.8168 (t0) REVERT: K 92 ASP cc_start: 0.9315 (m-30) cc_final: 0.8880 (m-30) REVERT: L 81 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8419 (mp10) REVERT: L 85 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8335 (mm-30) REVERT: O 46 GLU cc_start: 0.8472 (mp0) cc_final: 0.8003 (mp0) REVERT: I 100 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8683 (mt-10) REVERT: I 112 GLU cc_start: 0.8145 (mp0) cc_final: 0.7797 (mp0) REVERT: J 544 THR cc_start: 0.9424 (m) cc_final: 0.9063 (p) REVERT: J 595 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8777 (tt0) REVERT: D 106 GLU cc_start: 0.8904 (tp30) cc_final: 0.8677 (tp30) REVERT: D 112 GLU cc_start: 0.8109 (mp0) cc_final: 0.7772 (mp0) REVERT: E 523 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: M 100 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8667 (pt0) REVERT: M 106 GLU cc_start: 0.8882 (tp30) cc_final: 0.8619 (tp30) REVERT: M 112 GLU cc_start: 0.8254 (mp0) cc_final: 0.7920 (mp0) REVERT: N 595 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8642 (tt0) outliers start: 40 outliers final: 28 residues processed: 345 average time/residue: 1.5844 time to fit residues: 598.1141 Evaluate side-chains 349 residues out of total 1779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 103 ARG Chi-restraints excluded: chain F residue 106 TYR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 106 TYR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 597 TRP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 597 TRP Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 178 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3581 > 50: distance: 37 - 44: 3.195 distance: 44 - 45: 11.088 distance: 45 - 46: 19.071 distance: 45 - 48: 12.749 distance: 46 - 47: 14.271 distance: 46 - 49: 23.424 distance: 49 - 50: 11.113 distance: 50 - 51: 14.391 distance: 50 - 53: 11.987 distance: 51 - 52: 11.447 distance: 53 - 54: 20.805 distance: 54 - 55: 5.963 distance: 55 - 56: 8.359 distance: 55 - 57: 14.041 distance: 58 - 59: 8.786 distance: 59 - 60: 29.803 distance: 59 - 62: 13.968 distance: 60 - 61: 14.964 distance: 60 - 66: 31.528 distance: 62 - 63: 12.585 distance: 63 - 64: 12.265 distance: 63 - 65: 27.148 distance: 66 - 67: 17.180 distance: 67 - 68: 28.572 distance: 67 - 70: 13.816 distance: 68 - 69: 16.325 distance: 68 - 72: 24.584 distance: 70 - 71: 28.967 distance: 71 - 168: 8.558 distance: 72 - 73: 9.978 distance: 73 - 74: 8.813 distance: 73 - 76: 21.206 distance: 74 - 75: 16.761 distance: 74 - 84: 9.000 distance: 76 - 77: 6.169 distance: 77 - 78: 11.845 distance: 77 - 79: 12.784 distance: 78 - 80: 16.859 distance: 79 - 81: 12.141 distance: 80 - 82: 8.227 distance: 81 - 82: 16.223 distance: 82 - 83: 7.951 distance: 84 - 85: 15.093 distance: 85 - 86: 18.881 distance: 85 - 88: 10.490 distance: 86 - 87: 8.258 distance: 86 - 92: 26.698 distance: 88 - 89: 14.037 distance: 89 - 90: 12.574 distance: 89 - 91: 15.434 distance: 92 - 93: 5.260 distance: 93 - 94: 12.208 distance: 93 - 96: 12.170 distance: 94 - 95: 32.624 distance: 94 - 100: 40.447 distance: 96 - 97: 15.789 distance: 97 - 98: 58.247 distance: 97 - 99: 29.462 distance: 100 - 101: 18.713 distance: 101 - 102: 23.580 distance: 101 - 104: 8.641 distance: 102 - 109: 42.124 distance: 104 - 105: 3.388 distance: 105 - 106: 18.078 distance: 106 - 107: 7.850 distance: 106 - 108: 23.975 distance: 109 - 110: 37.005 distance: 110 - 111: 23.762 distance: 110 - 113: 7.201 distance: 111 - 112: 8.858 distance: 111 - 117: 40.156 distance: 113 - 114: 30.964 distance: 114 - 116: 25.360 distance: 117 - 118: 8.886 distance: 118 - 119: 12.244 distance: 118 - 121: 5.932 distance: 119 - 120: 14.070 distance: 119 - 126: 7.327 distance: 121 - 122: 9.959 distance: 122 - 123: 15.524 distance: 123 - 124: 15.851 distance: 124 - 125: 54.560