Starting phenix.real_space_refine on Tue Aug 6 04:59:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucv_20729/08_2024/6ucv_20729.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 9682 2.51 5 N 2523 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "I ARG 52": "NH1" <-> "NH2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 219": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 330": "NH1" <-> "NH2" Residue "J ARG 89": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 219": "NH1" <-> "NH2" Residue "a ARG 235": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "i ARG 52": "NH1" <-> "NH2" Residue "i PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 219": "NH1" <-> "NH2" Residue "i ARG 235": "NH1" <-> "NH2" Residue "i ARG 330": "NH1" <-> "NH2" Residue "j ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15102 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2399 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2419 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "b" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 397 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "i" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "j" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "k" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "m" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.07, per 1000 atoms: 0.60 Number of scatterers: 15102 At special positions: 0 Unit cell: (100.05, 120.75, 215.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 2851 8.00 N 2523 7.00 C 9682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.7 seconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 37.5% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.135A pdb=" N GLN A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.638A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.638A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.917A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 31 Processing helix chain 'E' and resid 31 through 43 Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.652A pdb=" N LEU E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 56 removed outlier: 4.050A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.689A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 removed outlier: 3.625A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 58 removed outlier: 3.913A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 31 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 49 through 55 removed outlier: 3.504A pdb=" N LEU M 54 " --> pdb=" O PHE M 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 54 Processing helix chain 'a' and resid 364 through 373 removed outlier: 3.754A pdb=" N GLN a 372 " --> pdb=" O LEU a 368 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 135 Proline residue: b 112 - end of helix Processing helix chain 'c' and resid 14 through 49 Proline residue: c 39 - end of helix Processing helix chain 'd' and resid 29 through 51 removed outlier: 4.031A pdb=" N THR d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 58 removed outlier: 3.886A pdb=" N ASP d 55 " --> pdb=" O SER d 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 31 Processing helix chain 'e' and resid 31 through 43 removed outlier: 3.552A pdb=" N PHE e 35 " --> pdb=" O GLY e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 55 removed outlier: 3.692A pdb=" N LEU e 54 " --> pdb=" O PHE e 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 55 Processing helix chain 'i' and resid 67 through 72 removed outlier: 3.512A pdb=" N ARG i 72 " --> pdb=" O LYS i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 364 through 373 removed outlier: 3.581A pdb=" N GLN i 372 " --> pdb=" O LEU i 368 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 135 Proline residue: j 112 - end of helix Processing helix chain 'k' and resid 14 through 49 Proline residue: k 39 - end of helix removed outlier: 3.512A pdb=" N TRP k 49 " --> pdb=" O VAL k 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 51 removed outlier: 3.641A pdb=" N THR l 34 " --> pdb=" O SER l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 57 removed outlier: 4.068A pdb=" N ASP l 55 " --> pdb=" O SER l 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 31 Processing helix chain 'm' and resid 31 through 43 Processing helix chain 'm' and resid 49 through 55 removed outlier: 3.512A pdb=" N LEU m 54 " --> pdb=" O PHE m 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.971A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY A 83 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU A 357 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 85 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE A 359 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP A 87 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR A 361 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN A 89 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93 removed outlier: 6.851A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY I 83 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU I 357 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 93 removed outlier: 6.886A pdb=" N PHE a 98 " --> pdb=" O PHE a 92 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N CYS a 165 " --> pdb=" O ASN a 184 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR a 194 " --> pdb=" O PRO a 185 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS a 323 " --> pdb=" O ASP a 319 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG a 85 " --> pdb=" O LEU a 357 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE a 359 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP a 87 " --> pdb=" O PHE a 359 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR a 361 " --> pdb=" O ASP a 87 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN a 89 " --> pdb=" O THR a 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 83 through 93 removed outlier: 6.787A pdb=" N PHE i 98 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N CYS i 165 " --> pdb=" O ASN i 184 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR i 194 " --> pdb=" O PRO i 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS i 323 " --> pdb=" O ASP i 319 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY i 83 " --> pdb=" O CYS i 355 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU i 357 " --> pdb=" O GLY i 83 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG i 85 " --> pdb=" O LEU i 357 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE i 359 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP i 87 " --> pdb=" O PHE i 359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR i 361 " --> pdb=" O ASP i 87 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN i 89 " --> pdb=" O THR i 361 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3171 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: 5.48 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2487 1.30 - 1.43: 4065 1.43 - 1.56: 8770 1.56 - 1.69: 24 1.69 - 1.81: 72 Bond restraints: 15418 Sorted by residual: bond pdb=" C31 MC3 I 401 " pdb=" O2 MC3 I 401 " ideal model delta sigma weight residual 1.328 1.433 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C31 MC3 i 401 " pdb=" O2 MC3 i 401 " ideal model delta sigma weight residual 1.328 1.432 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C11 MC3 i 401 " pdb=" O3 MC3 i 401 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 MC3 I 401 " pdb=" O3 MC3 I 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N MC3 i 401 " pdb=" C8 MC3 i 401 " ideal model delta sigma weight residual 1.493 1.429 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 15413 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 416 107.06 - 113.80: 8641 113.80 - 120.53: 5925 120.53 - 127.27: 5776 127.27 - 134.00: 157 Bond angle restraints: 20915 Sorted by residual: angle pdb=" O1P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O2P MC3 i 401 " ideal model delta sigma weight residual 119.69 100.88 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" O1P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O2P MC3 I 401 " ideal model delta sigma weight residual 119.69 101.69 18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" O3P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O4P MC3 I 401 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O3P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O4P MC3 i 401 " ideal model delta sigma weight residual 93.26 109.81 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" CA ASP a 134 " pdb=" CB ASP a 134 " pdb=" CG ASP a 134 " ideal model delta sigma weight residual 112.60 117.22 -4.62 1.00e+00 1.00e+00 2.13e+01 ... (remaining 20910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.82: 8797 19.82 - 39.64: 259 39.64 - 59.46: 58 59.46 - 79.27: 2 79.27 - 99.09: 1 Dihedral angle restraints: 9117 sinusoidal: 3494 harmonic: 5623 Sorted by residual: dihedral pdb=" CA ASN i 95 " pdb=" C ASN i 95 " pdb=" N PRO i 96 " pdb=" CA PRO i 96 " ideal model delta harmonic sigma weight residual 180.00 139.35 40.65 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA ASN a 95 " pdb=" C ASN a 95 " pdb=" N PRO a 96 " pdb=" CA PRO a 96 " ideal model delta harmonic sigma weight residual 180.00 139.79 40.21 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 140.83 39.17 0 5.00e+00 4.00e-02 6.14e+01 ... (remaining 9114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2100 0.078 - 0.156: 256 0.156 - 0.234: 18 0.234 - 0.312: 2 0.312 - 0.390: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CB ILE m 33 " pdb=" CA ILE m 33 " pdb=" CG1 ILE m 33 " pdb=" CG2 ILE m 33 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE M 33 " pdb=" CA ILE M 33 " pdb=" CG1 ILE M 33 " pdb=" CG2 ILE M 33 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB ILE e 33 " pdb=" CA ILE e 33 " pdb=" CG1 ILE e 33 " pdb=" CG2 ILE e 33 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2377 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO A 207 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR a 206 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO a 207 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO a 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 207 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 206 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO I 207 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " 0.036 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1409 2.75 - 3.29: 13753 3.29 - 3.82: 24101 3.82 - 4.36: 26697 4.36 - 4.90: 48932 Nonbonded interactions: 114892 Sorted by model distance: nonbonded pdb=" OD1 ASN a 179 " pdb=" OG SER a 200 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASN i 179 " pdb=" OG SER i 200 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 312 " pdb=" OG SER B 116 " model vdw 2.279 3.040 ... (remaining 114887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 49 through 373) selection = (chain 'I' and resid 49 through 373) selection = (chain 'a' and resid 49 through 373) selection = (chain 'i' and resid 49 through 373) } ncs_group { reference = chain 'B' selection = (chain 'J' and resid 86 through 135) selection = (chain 'b' and resid 86 through 135) selection = chain 'j' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'D' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) selection = (chain 'L' and resid 27 through 61) selection = (chain 'd' and resid 27 through 61) selection = (chain 'l' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'e' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.620 Find NCS groups from input model: 0.790 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.005 0.105 15418 Z= 0.343 Angle : 0.941 18.813 20915 Z= 0.481 Chirality : 0.053 0.390 2380 Planarity : 0.007 0.067 2661 Dihedral : 10.415 99.092 5473 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.87 (0.17), residues: 1899 helix: -1.31 (0.14), residues: 724 sheet: -0.34 (0.18), residues: 808 loop : -2.50 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 100 HIS 0.005 0.001 HIS C 43 PHE 0.025 0.002 PHE b 92 TYR 0.015 0.002 TYR E 30 ARG 0.006 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9115 (tp) cc_final: 0.8831 (tp) REVERT: A 170 ASP cc_start: 0.8507 (t0) cc_final: 0.8262 (m-30) REVERT: A 171 TYR cc_start: 0.8367 (t80) cc_final: 0.8137 (t80) REVERT: I 369 MET cc_start: 0.8764 (mtp) cc_final: 0.8481 (tmm) REVERT: K 40 MET cc_start: 0.7006 (mpm) cc_final: 0.6411 (mpp) REVERT: M 54 LEU cc_start: 0.8884 (mp) cc_final: 0.8591 (tt) REVERT: a 303 ILE cc_start: 0.9077 (tt) cc_final: 0.8798 (mp) REVERT: e 38 TYR cc_start: 0.7540 (t80) cc_final: 0.6442 (m-80) REVERT: m 53 LEU cc_start: 0.8775 (tt) cc_final: 0.8465 (mt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2142 time to fit residues: 70.1634 Evaluate side-chains 84 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN C 17 HIS D 50 GLN E 29 HIS I 65 ASN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS M 29 HIS M 52 ASN a 65 ASN a 99 GLN c 17 HIS e 52 ASN i 99 GLN k 17 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15418 Z= 0.302 Angle : 0.652 7.715 20915 Z= 0.340 Chirality : 0.041 0.167 2380 Planarity : 0.005 0.056 2661 Dihedral : 7.569 95.508 2109 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % 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: -0.02 (0.19), residues: 1899 helix: 1.34 (0.18), residues: 720 sheet: -0.26 (0.18), residues: 817 loop : -1.87 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP j 100 HIS 0.008 0.001 HIS A 102 PHE 0.021 0.002 PHE C 34 TYR 0.013 0.002 TYR E 30 ARG 0.004 0.000 ARG i 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: A 369 MET cc_start: 0.8094 (tpt) cc_final: 0.7774 (tpp) REVERT: C 40 MET cc_start: 0.8460 (mpp) cc_final: 0.7982 (mpp) REVERT: M 54 LEU cc_start: 0.9269 (mp) cc_final: 0.8769 (tt) REVERT: m 53 LEU cc_start: 0.8677 (tt) cc_final: 0.8432 (mt) outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.2127 time to fit residues: 36.2163 Evaluate side-chains 65 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 65 ASN i 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15418 Z= 0.234 Angle : 0.606 7.813 20915 Z= 0.314 Chirality : 0.041 0.154 2380 Planarity : 0.004 0.055 2661 Dihedral : 7.121 83.646 2109 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.67 (0.20), residues: 1899 helix: 2.22 (0.19), residues: 719 sheet: -0.22 (0.18), residues: 815 loop : -1.39 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 36 HIS 0.005 0.001 HIS A 102 PHE 0.018 0.001 PHE C 34 TYR 0.011 0.001 TYR E 30 ARG 0.004 0.000 ARG I 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8721 (pm20) cc_final: 0.8498 (pp20) REVERT: A 369 MET cc_start: 0.8101 (tpt) cc_final: 0.7780 (tpp) REVERT: C 40 MET cc_start: 0.8389 (mpp) cc_final: 0.7965 (mpp) REVERT: I 369 MET cc_start: 0.8450 (tmm) cc_final: 0.8156 (tmm) REVERT: M 54 LEU cc_start: 0.9269 (mp) cc_final: 0.8764 (tt) REVERT: a 303 ILE cc_start: 0.9302 (tt) cc_final: 0.9001 (mp) REVERT: m 53 LEU cc_start: 0.8788 (tt) cc_final: 0.8516 (mt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1913 time to fit residues: 28.7521 Evaluate side-chains 66 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN d 38 ASN e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15418 Z= 0.245 Angle : 0.610 8.023 20915 Z= 0.313 Chirality : 0.040 0.148 2380 Planarity : 0.004 0.052 2661 Dihedral : 7.026 67.117 2109 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.05 (0.20), residues: 1899 helix: 2.64 (0.19), residues: 720 sheet: -0.18 (0.18), residues: 816 loop : -1.01 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 32 HIS 0.006 0.001 HIS A 102 PHE 0.017 0.001 PHE i 359 TYR 0.015 0.001 TYR I 307 ARG 0.003 0.000 ARG I 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8511 (mpp) cc_final: 0.8207 (mpp) REVERT: D 54 MET cc_start: 0.8224 (tpp) cc_final: 0.7684 (tpp) REVERT: I 79 TYR cc_start: 0.8866 (m-80) cc_final: 0.8636 (m-80) REVERT: I 369 MET cc_start: 0.8413 (tmm) cc_final: 0.8116 (tmm) REVERT: M 54 LEU cc_start: 0.9267 (mp) cc_final: 0.8820 (tt) REVERT: a 94 MET cc_start: 0.8427 (mmm) cc_final: 0.8220 (mmm) REVERT: b 127 GLU cc_start: 0.8408 (pp20) cc_final: 0.7719 (tm-30) REVERT: m 53 LEU cc_start: 0.8700 (tt) cc_final: 0.8454 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2024 time to fit residues: 28.3791 Evaluate side-chains 65 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN M 52 ASN a 99 GLN e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15418 Z= 0.167 Angle : 0.573 7.852 20915 Z= 0.290 Chirality : 0.040 0.155 2380 Planarity : 0.004 0.051 2661 Dihedral : 6.685 65.171 2109 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1899 helix: 2.83 (0.19), residues: 720 sheet: -0.10 (0.18), residues: 815 loop : -0.82 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 32 HIS 0.010 0.001 HIS i 51 PHE 0.013 0.001 PHE J 130 TYR 0.011 0.001 TYR I 307 ARG 0.002 0.000 ARG i 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8437 (pp20) REVERT: C 40 MET cc_start: 0.8433 (mpp) cc_final: 0.8171 (mpp) REVERT: D 54 MET cc_start: 0.8205 (tpp) cc_final: 0.7666 (tpp) REVERT: I 369 MET cc_start: 0.8430 (tmm) cc_final: 0.8111 (tmm) REVERT: K 40 MET cc_start: 0.8384 (mpp) cc_final: 0.8105 (mpp) REVERT: M 54 LEU cc_start: 0.9222 (mp) cc_final: 0.8829 (tt) REVERT: b 127 GLU cc_start: 0.8443 (pp20) cc_final: 0.7842 (tm-30) REVERT: b 131 ASP cc_start: 0.8381 (m-30) cc_final: 0.7500 (m-30) REVERT: c 40 MET cc_start: 0.8807 (mpp) cc_final: 0.8539 (mpp) REVERT: l 54 MET cc_start: 0.9300 (tpp) cc_final: 0.9079 (tpp) REVERT: m 53 LEU cc_start: 0.8711 (tt) cc_final: 0.8477 (mt) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.2016 time to fit residues: 30.3702 Evaluate side-chains 63 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 6.9990 chunk 162 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 94 optimal weight: 40.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN E 52 ASN I 99 GLN I 166 GLN I 172 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN a 208 GLN e 52 ASN m 52 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15418 Z= 0.353 Angle : 0.674 8.148 20915 Z= 0.350 Chirality : 0.042 0.148 2380 Planarity : 0.004 0.050 2661 Dihedral : 7.258 65.335 2109 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.11 (0.20), residues: 1899 helix: 2.74 (0.19), residues: 723 sheet: -0.21 (0.18), residues: 805 loop : -0.95 (0.36), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP m 41 HIS 0.008 0.001 HIS i 51 PHE 0.017 0.002 PHE A 359 TYR 0.021 0.002 TYR E 30 ARG 0.005 0.001 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8030 (tpt) cc_final: 0.7798 (tpp) REVERT: C 37 VAL cc_start: 0.9088 (m) cc_final: 0.8554 (p) REVERT: C 40 MET cc_start: 0.8682 (mpp) cc_final: 0.8053 (mpp) REVERT: D 54 MET cc_start: 0.8242 (tpp) cc_final: 0.7874 (tpp) REVERT: I 369 MET cc_start: 0.8459 (tmm) cc_final: 0.7945 (tmm) REVERT: M 54 LEU cc_start: 0.9159 (mp) cc_final: 0.8811 (tt) REVERT: c 40 MET cc_start: 0.8963 (mpp) cc_final: 0.8683 (mpp) REVERT: m 53 LEU cc_start: 0.8748 (tt) cc_final: 0.8476 (mt) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1995 time to fit residues: 25.9218 Evaluate side-chains 58 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15418 Z= 0.240 Angle : 0.616 9.191 20915 Z= 0.317 Chirality : 0.041 0.156 2380 Planarity : 0.004 0.050 2661 Dihedral : 6.855 65.338 2109 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.21 (0.20), residues: 1899 helix: 2.85 (0.19), residues: 723 sheet: -0.23 (0.18), residues: 805 loop : -0.79 (0.36), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 41 HIS 0.005 0.001 HIS A 102 PHE 0.015 0.001 PHE B 130 TYR 0.019 0.001 TYR I 307 ARG 0.005 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8064 (tpt) cc_final: 0.7838 (tpp) REVERT: D 54 MET cc_start: 0.8221 (tpp) cc_final: 0.7862 (tpp) REVERT: I 369 MET cc_start: 0.8488 (tmm) cc_final: 0.8140 (tmm) REVERT: M 54 LEU cc_start: 0.9133 (mp) cc_final: 0.8770 (tt) REVERT: b 127 GLU cc_start: 0.8586 (pp20) cc_final: 0.7972 (tm-30) REVERT: c 40 MET cc_start: 0.8995 (mpp) cc_final: 0.8700 (mpp) REVERT: l 54 MET cc_start: 0.9302 (tpp) cc_final: 0.9058 (tpp) REVERT: m 53 LEU cc_start: 0.8703 (tt) cc_final: 0.8429 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2071 time to fit residues: 27.3445 Evaluate side-chains 59 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 0.0270 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15418 Z= 0.216 Angle : 0.604 8.200 20915 Z= 0.309 Chirality : 0.041 0.202 2380 Planarity : 0.004 0.049 2661 Dihedral : 6.676 62.527 2109 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.30 (0.21), residues: 1899 helix: 2.93 (0.19), residues: 723 sheet: -0.22 (0.18), residues: 804 loop : -0.65 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 41 HIS 0.004 0.001 HIS A 102 PHE 0.018 0.001 PHE A 359 TYR 0.015 0.001 TYR I 307 ARG 0.004 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8049 (tpt) cc_final: 0.7817 (tpp) REVERT: D 54 MET cc_start: 0.8222 (tpp) cc_final: 0.7864 (tpp) REVERT: I 369 MET cc_start: 0.8505 (tmm) cc_final: 0.7925 (tmm) REVERT: M 54 LEU cc_start: 0.9080 (mp) cc_final: 0.8763 (tt) REVERT: b 127 GLU cc_start: 0.8556 (pp20) cc_final: 0.8169 (tm-30) REVERT: l 54 MET cc_start: 0.9292 (tpp) cc_final: 0.9064 (tpp) REVERT: m 53 LEU cc_start: 0.8742 (tt) cc_final: 0.8465 (mt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2122 time to fit residues: 26.9831 Evaluate side-chains 60 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15418 Z= 0.257 Angle : 0.626 7.962 20915 Z= 0.321 Chirality : 0.041 0.200 2380 Planarity : 0.004 0.048 2661 Dihedral : 6.784 62.207 2109 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.23 (0.21), residues: 1899 helix: 2.89 (0.19), residues: 723 sheet: -0.26 (0.18), residues: 801 loop : -0.73 (0.37), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 41 HIS 0.006 0.001 HIS i 51 PHE 0.017 0.001 PHE A 340 TYR 0.013 0.001 TYR I 307 ARG 0.004 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8084 (tpt) cc_final: 0.7853 (tpp) REVERT: C 40 MET cc_start: 0.8238 (mpp) cc_final: 0.8025 (mpp) REVERT: D 54 MET cc_start: 0.8258 (tpp) cc_final: 0.7894 (tpp) REVERT: I 369 MET cc_start: 0.8504 (tmm) cc_final: 0.7958 (tmm) REVERT: M 54 LEU cc_start: 0.9119 (mp) cc_final: 0.8819 (tt) REVERT: c 40 MET cc_start: 0.8784 (mpp) cc_final: 0.8327 (mpp) REVERT: l 54 MET cc_start: 0.9298 (tpp) cc_final: 0.9066 (tpp) REVERT: m 53 LEU cc_start: 0.8711 (tt) cc_final: 0.8470 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2076 time to fit residues: 26.5355 Evaluate side-chains 59 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 HIS M 52 ASN e 52 ASN m 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15418 Z= 0.365 Angle : 0.706 9.255 20915 Z= 0.366 Chirality : 0.043 0.180 2380 Planarity : 0.004 0.047 2661 Dihedral : 7.203 65.803 2109 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.91 (0.20), residues: 1899 helix: 2.67 (0.19), residues: 720 sheet: -0.46 (0.18), residues: 805 loop : -0.87 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP m 41 HIS 0.009 0.001 HIS A 102 PHE 0.024 0.002 PHE A 359 TYR 0.023 0.002 TYR I 307 ARG 0.006 0.001 ARG I 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8073 (tpt) cc_final: 0.7829 (tpp) REVERT: D 54 MET cc_start: 0.8332 (tpp) cc_final: 0.7972 (tpp) REVERT: M 54 LEU cc_start: 0.9159 (mp) cc_final: 0.8907 (tt) REVERT: l 54 MET cc_start: 0.9290 (tpp) cc_final: 0.9057 (tpp) REVERT: m 53 LEU cc_start: 0.8765 (tt) cc_final: 0.8493 (mt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2157 time to fit residues: 25.1892 Evaluate side-chains 58 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2373 > 50: distance: 14 - 47: 12.910 distance: 17 - 44: 9.052 distance: 28 - 38: 5.195 distance: 38 - 39: 9.943 distance: 38 - 99: 6.323 distance: 39 - 40: 6.542 distance: 39 - 42: 7.622 distance: 40 - 41: 10.028 distance: 40 - 44: 4.549 distance: 41 - 96: 13.943 distance: 42 - 43: 8.314 distance: 44 - 45: 3.583 distance: 45 - 46: 8.691 distance: 45 - 48: 5.518 distance: 46 - 47: 9.133 distance: 46 - 55: 10.175 distance: 48 - 49: 5.856 distance: 49 - 50: 9.551 distance: 51 - 52: 4.689 distance: 52 - 53: 4.417 distance: 52 - 54: 12.820 distance: 55 - 56: 7.670 distance: 56 - 57: 3.427 distance: 56 - 59: 7.982 distance: 57 - 58: 3.193 distance: 57 - 62: 4.868 distance: 59 - 60: 3.862 distance: 59 - 61: 9.235 distance: 62 - 63: 9.453 distance: 63 - 64: 4.779 distance: 63 - 66: 4.567 distance: 66 - 67: 4.694 distance: 67 - 68: 7.772 distance: 67 - 69: 10.541 distance: 70 - 71: 7.227 distance: 71 - 72: 9.758 distance: 72 - 73: 17.848 distance: 72 - 74: 10.204 distance: 74 - 75: 8.270 distance: 75 - 76: 10.960 distance: 75 - 78: 5.851 distance: 76 - 77: 15.114 distance: 76 - 80: 27.905 distance: 78 - 79: 7.961 distance: 80 - 81: 29.633 distance: 81 - 82: 18.843 distance: 81 - 84: 28.416 distance: 82 - 83: 23.644 distance: 82 - 85: 6.937 distance: 85 - 86: 14.007 distance: 85 - 91: 4.465 distance: 86 - 87: 11.646 distance: 86 - 89: 5.087 distance: 87 - 88: 26.143 distance: 87 - 92: 12.763 distance: 89 - 90: 11.088 distance: 90 - 91: 13.153 distance: 92 - 93: 11.457 distance: 93 - 94: 20.698 distance: 94 - 95: 21.765 distance: 94 - 96: 7.954 distance: 96 - 97: 8.261 distance: 97 - 98: 4.457 distance: 97 - 100: 14.791 distance: 98 - 99: 3.851 distance: 98 - 104: 3.522 distance: 100 - 101: 9.532 distance: 101 - 102: 3.782 distance: 101 - 103: 3.171