Starting phenix.real_space_refine on Sun Sep 29 05:05:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_27637.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_27637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_27637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_27637.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpl_27637/09_2024/8dpl_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-5461/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: 9.87, per 1000 atoms: 0.58 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: 4.37 Conformation dependent library (CDL) restraints added in 2.3 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: 3.13 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: 5.62 Time building geometry restraints manager: 5.10 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.810 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.100 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 1.853 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: 1.4610 time to fit residues: 812.5159 Evaluate side-chains 340 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 334 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 fitting. rotamer outliers: 38 poor density : 346 time to evaluate : 1.949 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: G 85 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 85 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 221 MET cc_start: 0.6040 (mmt) cc_final: 0.5605 (mmt) REVERT: K 46 GLU cc_start: 0.7669 (tt0) cc_final: 0.7468 (tt0) REVERT: L 85 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7824 (mm-30) REVERT: J 523 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: D 228 ASN cc_start: 0.8558 (p0) cc_final: 0.8356 (p0) REVERT: E 523 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: M 136 ARG cc_start: 0.7495 (tpt90) cc_final: 0.6827 (tpm170) outliers start: 38 outliers final: 20 residues processed: 362 average time/residue: 1.5282 time to fit residues: 603.7595 Evaluate side-chains 329 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 307 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 28 ASN H 6 GLN A 31 ASN A 105 ASN O 6 GLN I 44 GLN J 595 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17271 Z= 0.312 Angle : 0.642 7.875 23463 Z= 0.325 Chirality : 0.044 0.172 2628 Planarity : 0.005 0.077 2967 Dihedral : 8.216 75.670 2765 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 14.81 % Favored : 83.00 % 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: 0.77 (0.18), residues: 2115 helix: 2.29 (0.40), residues: 156 sheet: 0.81 (0.17), residues: 918 loop : 0.05 (0.19), residues: 1041 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 0.014 0.001 PHE F 97 TYR 0.014 0.001 TYR K 104 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 383 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 344 time to evaluate : 1.935 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 103 ARG cc_start: 0.7472 (ttp80) cc_final: 0.5247 (ttp80) REVERT: F 107 ASP cc_start: 0.7028 (p0) cc_final: 0.6611 (p0) REVERT: G 85 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 103 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6545 (ttp80) REVERT: B 85 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8127 (mm-30) REVERT: B 98 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7877 (mpp80) REVERT: C 221 MET cc_start: 0.5874 (mmt) cc_final: 0.5456 (mmt) REVERT: J 523 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: D 156 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: E 523 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: M 214 TYR cc_start: 0.6607 (p90) cc_final: 0.6334 (p90) REVERT: N 523 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6387 (pt0) outliers start: 39 outliers final: 17 residues processed: 361 average time/residue: 1.4850 time to fit residues: 585.8890 Evaluate side-chains 334 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 313 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 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 A residue 51 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 142 VAL Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 523 GLU 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 M residue 55 ASP 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 188 optimal weight: 0.0980 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 0.0010 chunk 181 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17271 Z= 0.177 Angle : 0.629 8.628 23463 Z= 0.317 Chirality : 0.044 0.172 2628 Planarity : 0.005 0.099 2967 Dihedral : 7.798 69.974 2763 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.75 % Allowed : 15.43 % Favored : 82.83 % 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: 0.78 (0.18), residues: 2115 helix: 2.54 (0.40), residues: 156 sheet: 0.86 (0.17), residues: 921 loop : -0.04 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS H 229 PHE 0.013 0.001 PHE O 148 TYR 0.021 0.001 TYR G 51 ARG 0.009 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 379 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 1.972 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 103 ARG cc_start: 0.7118 (ttp80) cc_final: 0.6634 (ttp80) REVERT: F 107 ASP cc_start: 0.7083 (p0) cc_final: 0.6784 (p0) REVERT: G 17 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7203 (ttp80) REVERT: G 85 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 92 ASP cc_start: 0.8859 (m-30) cc_final: 0.8643 (m-30) REVERT: A 103 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6709 (ttp80) REVERT: B 85 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8195 (mm-30) REVERT: C 221 MET cc_start: 0.5835 (mmt) cc_final: 0.5432 (mmt) REVERT: K 75 ASP cc_start: 0.8335 (t0) cc_final: 0.7777 (t0) REVERT: D 136 ARG cc_start: 0.7519 (tpm-80) cc_final: 0.7130 (tpm170) REVERT: E 523 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6817 (pt0) outliers start: 31 outliers final: 14 residues processed: 361 average time/residue: 1.4967 time to fit residues: 591.3288 Evaluate side-chains 334 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 319 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 106 TYR 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 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 E residue 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain N residue 544 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 182 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** J 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17271 Z= 0.197 Angle : 0.649 8.534 23463 Z= 0.326 Chirality : 0.044 0.171 2628 Planarity : 0.005 0.092 2967 Dihedral : 7.625 67.990 2763 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.14 % Allowed : 16.89 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2115 helix: 2.70 (0.41), residues: 156 sheet: 0.81 (0.17), residues: 930 loop : -0.09 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 47 HIS 0.004 0.001 HIS H 229 PHE 0.011 0.001 PHE H 148 TYR 0.024 0.001 TYR G 51 ARG 0.010 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 373 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 335 time to evaluate : 1.769 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 107 ASP cc_start: 0.6988 (p0) cc_final: 0.6701 (p0) REVERT: G 17 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7792 (ttp80) REVERT: G 85 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 103 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7049 (ttp80) REVERT: B 85 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 221 MET cc_start: 0.5785 (mmt) cc_final: 0.5377 (mmt) REVERT: K 103 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7610 (ttp-110) REVERT: D 136 ARG cc_start: 0.7425 (tpm-80) cc_final: 0.7081 (tpm170) REVERT: N 523 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6883 (pt0) outliers start: 38 outliers final: 23 residues processed: 353 average time/residue: 1.4619 time to fit residues: 564.8799 Evaluate side-chains 334 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 310 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 142 VAL 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 K residue 106 TYR 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 544 THR 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 527 ILE Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain M residue 55 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 0.0070 chunk 106 optimal weight: 10.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN G 28 ASN A 31 ASN A 112 GLN K 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17271 Z= 0.371 Angle : 0.702 8.494 23463 Z= 0.354 Chirality : 0.045 0.173 2628 Planarity : 0.005 0.063 2967 Dihedral : 7.933 70.813 2763 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.87 % Allowed : 17.40 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2115 helix: 2.67 (0.41), residues: 156 sheet: 0.73 (0.17), residues: 921 loop : -0.20 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 47 HIS 0.007 0.001 HIS H 229 PHE 0.015 0.001 PHE A 97 TYR 0.028 0.002 TYR G 51 ARG 0.012 0.001 ARG J 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 373 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 322 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7857 (ttp80) REVERT: G 85 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 75 ASP cc_start: 0.7972 (t0) cc_final: 0.7699 (t0) REVERT: A 107 ASP cc_start: 0.6881 (p0) cc_final: 0.6538 (p0) REVERT: B 85 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8221 (mm-30) REVERT: C 221 MET cc_start: 0.5901 (mmt) cc_final: 0.5452 (mmt) REVERT: K 107 ASP cc_start: 0.7563 (m-30) cc_final: 0.7361 (m-30) REVERT: J 523 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: E 523 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: M 136 ARG cc_start: 0.7421 (tpt90) cc_final: 0.6939 (tpm170) REVERT: N 523 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7017 (pt0) outliers start: 51 outliers final: 24 residues processed: 347 average time/residue: 1.5133 time to fit residues: 574.2277 Evaluate side-chains 332 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR 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 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 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain K residue 55 THR 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 O residue 155 ASP 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 78 ASP 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 195 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17271 Z= 0.228 Angle : 0.711 9.082 23463 Z= 0.357 Chirality : 0.044 0.170 2628 Planarity : 0.005 0.061 2967 Dihedral : 7.568 66.013 2763 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 18.81 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2115 helix: 2.77 (0.41), residues: 156 sheet: 0.84 (0.17), residues: 885 loop : -0.17 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 47 HIS 0.005 0.001 HIS H 229 PHE 0.011 0.001 PHE A 97 TYR 0.027 0.001 TYR G 51 ARG 0.012 0.001 ARG O 156 *********************** 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 368 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 329 time to evaluate : 2.065 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: G 85 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 103 ARG cc_start: 0.7618 (ttp80) cc_final: 0.6977 (ttp80) REVERT: B 85 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8287 (mm-30) REVERT: C 221 MET cc_start: 0.5796 (mmt) cc_final: 0.5379 (mmt) REVERT: M 136 ARG cc_start: 0.7413 (tpt90) cc_final: 0.6958 (tpm170) REVERT: N 523 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7232 (pt0) outliers start: 39 outliers final: 26 residues processed: 350 average time/residue: 1.4955 time to fit residues: 573.2581 Evaluate side-chains 334 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 307 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR 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 61 ASP Chi-restraints excluded: chain K residue 76 ASP 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 O residue 166 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 178 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 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain M residue 78 ASP Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 576 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17271 Z= 0.378 Angle : 0.755 9.607 23463 Z= 0.381 Chirality : 0.046 0.172 2628 Planarity : 0.005 0.064 2967 Dihedral : 7.927 69.665 2763 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.91 % Allowed : 20.16 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.51 (0.18), residues: 2115 helix: 2.69 (0.42), residues: 156 sheet: 0.69 (0.17), residues: 903 loop : -0.29 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 47 HIS 0.008 0.001 HIS H 229 PHE 0.015 0.001 PHE H 148 TYR 0.030 0.002 TYR G 51 ARG 0.014 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 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 358 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 324 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 103 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7155 (ttp80) REVERT: C 221 MET cc_start: 0.5883 (mmt) cc_final: 0.5539 (mmt) REVERT: E 523 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: N 523 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7265 (pt0) outliers start: 34 outliers final: 26 residues processed: 341 average time/residue: 1.5167 time to fit residues: 565.1090 Evaluate side-chains 335 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 155 ASP 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 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ASP 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 I residue 178 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 78 ASP Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 0.0000 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17271 Z= 0.272 Angle : 0.756 10.132 23463 Z= 0.380 Chirality : 0.045 0.169 2628 Planarity : 0.005 0.065 2967 Dihedral : 7.666 66.567 2763 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.97 % Allowed : 20.50 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.79 (0.41), residues: 156 sheet: 0.75 (0.18), residues: 864 loop : -0.31 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 47 HIS 0.005 0.001 HIS O 229 PHE 0.011 0.001 PHE A 97 TYR 0.029 0.001 TYR G 51 ARG 0.014 0.001 ARG E 587 *********************** REFINEMENT MACRO_CYCLE 9 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 353 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 318 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 76 ASP cc_start: 0.7643 (m-30) cc_final: 0.7386 (m-30) REVERT: G 85 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 76 ASP cc_start: 0.7485 (m-30) cc_final: 0.6966 (m-30) REVERT: A 107 ASP cc_start: 0.6888 (p0) cc_final: 0.6621 (p0) REVERT: B 85 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8148 (tp30) REVERT: C 221 MET cc_start: 0.5864 (mmt) cc_final: 0.5576 (mmt) REVERT: N 523 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7235 (pt0) outliers start: 35 outliers final: 27 residues processed: 340 average time/residue: 1.5102 time to fit residues: 561.3349 Evaluate side-chains 338 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 310 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 100 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 100 THR 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 76 ASP Chi-restraints excluded: chain K residue 88 LEU 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 I residue 178 GLU 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 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.2794 ------------------------------------------------------------------------------- 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 105 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3650 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= 0.265 Angle : 0.773 10.463 23463 Z= 0.389 Chirality : 0.045 0.168 2628 Planarity : 0.006 0.071 2967 Dihedral : 7.625 65.542 2763 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.63 % Allowed : 21.28 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.54 (0.18), residues: 2115 helix: 2.86 (0.42), residues: 156 sheet: 0.75 (0.18), residues: 867 loop : -0.30 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.006 0.001 HIS O 229 PHE 0.015 0.001 PHE H 148 TYR 0.029 0.001 TYR G 51 ARG 0.015 0.001 ARG C 156 ********************** REFINEMENT MACRO_CYCLE 10 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 351 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 322 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 103 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7080 (ttp80) REVERT: B 85 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8081 (tp30) REVERT: C 221 MET cc_start: 0.5838 (mmt) cc_final: 0.5519 (mmt) REVERT: N 523 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6911 (pm20) outliers start: 29 outliers final: 27 residues processed: 338 average time/residue: 1.4880 time to fit residues: 550.1955 Evaluate side-chains 341 residues out of total 1779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 100 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 100 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 105 ASN 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 I residue 178 GLU 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 576 THR Chi-restraints excluded: chain M residue 55 ASP Chi-restraints excluded: chain N residue 523 GLU Chi-restraints excluded: chain N residue 544 THR Chi-restraints excluded: chain N residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 0.0000 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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** K 31 ASN O 144 GLN J 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045701 restraints weight = 45417.588| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.54 r_work: 0.2566 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17271 Z= 0.239 Angle : 0.783 10.491 23463 Z= 0.391 Chirality : 0.045 0.168 2628 Planarity : 0.005 0.062 2967 Dihedral : 7.405 62.894 2763 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.35 % Allowed : 21.62 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.55 (0.18), residues: 2115 helix: 2.92 (0.41), residues: 156 sheet: 0.76 (0.18), residues: 870 loop : -0.30 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.004 0.001 HIS H 229 PHE 0.010 0.001 PHE A 97 TYR 0.031 0.001 TYR G 51 ARG 0.015 0.001 ARG J 587 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8733.36 seconds wall clock time: 155 minutes 18.71 seconds (9318.71 seconds total)