Starting phenix.real_space_refine on Mon Sep 30 15:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugn_26490/09_2024/7ugn_26490_neut.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 16083 2.51 5 N 4329 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25698 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3552 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 426} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 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: 16.49, per 1000 atoms: 0.64 Number of scatterers: 25698 At special positions: 0 Unit cell: (151.445, 162.695, 157.503, 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 153 16.00 O 5133 8.00 N 4329 7.00 C 16083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 Atom "HETATM25461 O5 NAG p 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM25461 O5 NAG p 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " " MAN X 6 " - " MAN X 7 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 6 " " MAN f 4 " - " MAN f 5 " " MAN f 6 " - " MAN Q 201 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " MAN n 4 " - " MAN n 5 " " MAN n 6 " - " MAN n 7 " ALPHA1-6 " BMA U 3 " - " MAN U 5 " " BMA X 3 " - " MAN X 6 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 392 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 392 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG a 1 " - " ASN B 156 " " NAG b 1 " - " ASN B 234 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 295 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 332 " " NAG g 1 " - " ASN B 363 " " NAG i 1 " - " ASN C 156 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 262 " " NAG l 1 " - " ASN C 295 " " NAG m 1 " - " ASN C 301 " " NAG n 1 " - " ASN C 332 " " NAG o 1 " - " ASN C 363 " " NAG p 1 " - " ASN C 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 3.2 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 64 sheets defined 13.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.621A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.868A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.565A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.700A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.623A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.926A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.569A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.693A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.619A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.565A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.681A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.751A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.556A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 595 removed outlier: 3.975A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.691A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.564A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 595 removed outlier: 3.974A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.738A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 574 removed outlier: 3.558A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 595 removed outlier: 3.993A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.533A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.760A pdb=" N ASP G 86 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.773A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.766A pdb=" N ASP I 86 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.820A pdb=" N ASN L 33 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 34' Processing helix chain 'M' and resid 61 through 64 removed outlier: 4.141A pdb=" N ASN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.113A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 64 removed outlier: 4.174A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.064A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 4.017A pdb=" N ASN O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.831A pdb=" N THR O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.550A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.877A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.096A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.582A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.811A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 495 removed outlier: 3.538A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.876A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 7.119A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.585A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AB7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.825A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 307 Processing sheet with id=AC2, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 495 removed outlier: 3.535A pdb=" N GLY C 495 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 495 removed outlier: 3.535A pdb=" N GLY C 495 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.861A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.121A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.607A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AC9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.627A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.806A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD5, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.850A pdb=" N GLU G 10 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.850A pdb=" N GLU G 10 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.863A pdb=" N GLU I 10 " --> pdb=" O MET I 108 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.863A pdb=" N GLU I 10 " --> pdb=" O MET I 108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AE6, first strand: chain 'J' and resid 47 through 48 Processing sheet with id=AE7, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AE8, first strand: chain 'K' and resid 47 through 48 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'M' and resid 58 through 59 removed outlier: 4.168A pdb=" N THR M 58 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR M 50 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 95 through 100A Processing sheet with id=AF6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AF8, first strand: chain 'N' and resid 58 through 59 removed outlier: 4.150A pdb=" N THR N 58 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 50 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 95 through 100A Processing sheet with id=AG1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.689A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.175A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 95 through 100A Processing sheet with id=AG5, first strand: chain 'P' and resid 9 through 14 removed outlier: 6.449A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR P 105 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU P 107 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL P 13 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR P 102 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AG7, first strand: chain 'Q' and resid 9 through 14 removed outlier: 6.419A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR Q 105 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU Q 107 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL Q 13 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR Q 86 " --> pdb=" O THR Q 102 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AG9, first strand: chain 'R' and resid 9 through 14 removed outlier: 6.450A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU R 107 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL R 13 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR R 86 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 19 through 22 729 hydrogen bonds defined for protein. 1857 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: 10.34 Time building geometry restraints manager: 8.42 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: 8146 1.34 - 1.47: 6752 1.47 - 1.59: 11124 1.59 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 26238 Sorted by residual: bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C LYS B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.332 1.353 -0.020 8.90e-03 1.26e+04 5.20e+00 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.19e-02 7.06e+03 5.17e+00 ... (remaining 26233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 34990 2.10 - 4.20: 532 4.20 - 6.30: 88 6.30 - 8.40: 12 8.40 - 10.50: 6 Bond angle restraints: 35628 Sorted by residual: angle pdb=" C ARG Q 54 " pdb=" N PRO Q 55 " pdb=" CA PRO Q 55 " ideal model delta sigma weight residual 120.03 129.59 -9.56 9.90e-01 1.02e+00 9.32e+01 angle pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 120.03 128.29 -8.26 9.90e-01 1.02e+00 6.95e+01 angle pdb=" C ARG P 54 " pdb=" N PRO P 55 " pdb=" CA PRO P 55 " ideal model delta sigma weight residual 119.05 126.27 -7.22 1.11e+00 8.12e-01 4.24e+01 angle pdb=" N ASP Q 53 " pdb=" CA ASP Q 53 " pdb=" C ASP Q 53 " ideal model delta sigma weight residual 110.50 116.16 -5.66 1.41e+00 5.03e-01 1.61e+01 angle pdb=" N ASP P 53 " pdb=" CA ASP P 53 " pdb=" C ASP P 53 " ideal model delta sigma weight residual 109.23 115.16 -5.93 1.55e+00 4.16e-01 1.46e+01 ... (remaining 35623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.92: 15978 25.92 - 51.83: 574 51.83 - 77.75: 80 77.75 - 103.66: 70 103.66 - 129.58: 44 Dihedral angle restraints: 16746 sinusoidal: 7704 harmonic: 9042 Sorted by residual: dihedral pdb=" CA ARG Q 54 " pdb=" C ARG Q 54 " pdb=" N PRO Q 55 " pdb=" CA PRO Q 55 " ideal model delta harmonic sigma weight residual -180.00 -50.42 -129.58 0 5.00e+00 4.00e-02 6.72e+02 dihedral pdb=" CA ARG R 54 " pdb=" C ARG R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta harmonic sigma weight residual -180.00 -54.04 -125.96 0 5.00e+00 4.00e-02 6.35e+02 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " pdb=" CB CYS Q 88 " ideal model delta sinusoidal sigma weight residual -86.00 0.36 -86.36 1 1.00e+01 1.00e-02 8.99e+01 ... (remaining 16743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.943: 4176 0.943 - 1.887: 9 1.887 - 2.830: 11 2.830 - 3.773: 4 3.773 - 4.716: 1 Chirality restraints: 4201 Sorted by residual: chirality pdb=" C1 MAN n 6 " pdb=" O6 BMA n 3 " pdb=" C2 MAN n 6 " pdb=" O5 MAN n 6 " both_signs ideal model delta sigma weight residual False 2.40 -0.72 3.12 2.00e-02 2.50e+03 2.44e+04 chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 0.53 -2.93 2.00e-02 2.50e+03 2.15e+04 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 0.49 -2.89 2.00e-02 2.50e+03 2.08e+04 ... (remaining 4198 not shown) Planarity restraints: 4465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG p 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " -0.209 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 448 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG p 1 " 0.455 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 2 " -0.175 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" C7 NAG p 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG p 2 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG p 2 " 0.235 2.00e-02 2.50e+03 pdb=" O7 NAG p 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 4462 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.66: 5 1.66 - 2.47: 97 2.47 - 3.28: 25424 3.28 - 4.09: 56942 4.09 - 4.90: 104982 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187450 Sorted by model distance: nonbonded pdb=" CE1 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 0.844 3.340 nonbonded pdb=" CZ TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.292 3.260 nonbonded pdb=" ND2 ASN C 448 " pdb=" C5 NAG p 1 " model vdw 1.337 2.840 nonbonded pdb=" CZ TYR Q 49 " pdb=" OD2 ASP Q 53 " model vdw 1.528 3.260 nonbonded pdb=" CE1 TYR Q 49 " pdb=" OD2 ASP Q 53 " model vdw 1.542 3.340 ... (remaining 187445 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = (chain 'Q' and resid 8 through 108) selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'U' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'X' and (resid 2 or resid 5 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 6)) selection = (chain 'n' and (resid 2 or resid 5 through 7)) } 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: 9.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 60.390 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.240 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.050 26238 Z= 0.230 Angle : 0.654 10.497 35628 Z= 0.337 Chirality : 0.185 4.716 4201 Planarity : 0.006 0.297 4428 Dihedral : 15.930 129.579 10830 Min Nonbonded Distance : 0.844 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.11 % Allowed : 4.55 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % 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: -3.47 (0.13), residues: 3090 helix: -2.08 (0.24), residues: 357 sheet: -1.51 (0.15), residues: 1038 loop : -2.96 (0.12), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.002 0.000 HIS P 89 PHE 0.008 0.001 PHE C 383 TYR 0.010 0.001 TYR E 586 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7659 (tp30) cc_final: 0.7421 (tp30) REVERT: D 588 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7284 (ttm-80) REVERT: D 664 ASP cc_start: 0.6167 (m-30) cc_final: 0.5592 (p0) REVERT: E 664 ASP cc_start: 0.6577 (m-30) cc_final: 0.6164 (p0) REVERT: F 588 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7251 (ttm-80) REVERT: F 664 ASP cc_start: 0.6390 (m-30) cc_final: 0.6074 (p0) REVERT: I 61 GLN cc_start: 0.8028 (tp40) cc_final: 0.7610 (tm-30) REVERT: J 55 LYS cc_start: 0.7275 (mptt) cc_final: 0.7074 (mptt) REVERT: J 88 TYR cc_start: 0.7941 (m-80) cc_final: 0.7686 (m-80) REVERT: K 55 LYS cc_start: 0.7403 (mptt) cc_final: 0.7150 (mptt) REVERT: L 52 ASP cc_start: 0.7346 (m-30) cc_final: 0.6925 (m-30) REVERT: L 55 LYS cc_start: 0.7340 (mptt) cc_final: 0.6594 (mptt) REVERT: L 88 TYR cc_start: 0.8289 (m-80) cc_final: 0.8052 (m-80) REVERT: M 101 ASP cc_start: 0.7885 (p0) cc_final: 0.7572 (p0) REVERT: N 51 ILE cc_start: 0.8164 (tp) cc_final: 0.7933 (tp) REVERT: O 51 ILE cc_start: 0.8098 (tp) cc_final: 0.7700 (tp) REVERT: R 34 GLN cc_start: 0.8359 (mp-120) cc_final: 0.8005 (mp10) REVERT: R 85 ASP cc_start: 0.7032 (m-30) cc_final: 0.6361 (m-30) outliers start: 3 outliers final: 2 residues processed: 523 average time/residue: 0.4119 time to fit residues: 325.3243 Evaluate side-chains 369 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain P residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0000 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 0.0070 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 105 HIS A 258 GLN A 280 ASN A 411 ASN B 103 GLN B 105 HIS B 258 GLN B 280 ASN B 411 ASN C 103 GLN C 105 HIS C 258 GLN C 280 ASN C 411 ASN D 650 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN F 650 GLN F 653 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN J 6 GLN J 16 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS K 6 GLN K 16 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS L 6 GLN L 16 GLN M 64 ASN M 82AASN M 99 GLN N 99 GLN O 64 ASN P 52 GLN P 66CASN Q 66CASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26238 Z= 0.164 Angle : 0.637 17.611 35628 Z= 0.298 Chirality : 0.050 1.135 4201 Planarity : 0.004 0.088 4428 Dihedral : 13.084 106.632 5187 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.66 % Rotamer: Outliers : 1.66 % Allowed : 11.01 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 1.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3090 helix: -1.44 (0.25), residues: 381 sheet: -1.07 (0.15), residues: 1023 loop : -2.57 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 35 HIS 0.004 0.001 HIS K 41 PHE 0.023 0.001 PHE L 96 TYR 0.028 0.001 TYR L 51 ARG 0.025 0.001 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 404 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 TRP cc_start: 0.7684 (m-10) cc_final: 0.7364 (m-10) REVERT: D 588 ARG cc_start: 0.7573 (tpp80) cc_final: 0.7281 (ttm-80) REVERT: E 664 ASP cc_start: 0.6734 (m-30) cc_final: 0.6226 (p0) REVERT: F 588 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7042 (mtm-85) REVERT: F 664 ASP cc_start: 0.6386 (m-30) cc_final: 0.5970 (p0) REVERT: I 61 GLN cc_start: 0.8043 (tp40) cc_final: 0.7621 (tm-30) REVERT: J 52 ASP cc_start: 0.7417 (m-30) cc_final: 0.7197 (m-30) REVERT: J 88 TYR cc_start: 0.7948 (m-80) cc_final: 0.7710 (m-80) REVERT: L 55 LYS cc_start: 0.7391 (mptt) cc_final: 0.7041 (mptt) REVERT: L 88 TYR cc_start: 0.8201 (m-80) cc_final: 0.7973 (m-80) REVERT: M 100 MET cc_start: 0.8452 (mpp) cc_final: 0.8134 (mpp) REVERT: N 51 ILE cc_start: 0.8193 (tp) cc_final: 0.7926 (tp) REVERT: O 29 MET cc_start: 0.5377 (tmm) cc_final: 0.3771 (mmp) REVERT: O 51 ILE cc_start: 0.8103 (tp) cc_final: 0.7652 (tp) REVERT: P 79 GLU cc_start: 0.7591 (mp0) cc_final: 0.7310 (pm20) REVERT: R 34 GLN cc_start: 0.8436 (mp-120) cc_final: 0.7984 (mp10) outliers start: 45 outliers final: 25 residues processed: 430 average time/residue: 0.3845 time to fit residues: 254.7979 Evaluate side-chains 389 residues out of total 2712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 364 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 GLN Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain O residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 69.9252 > 50: distance: 28 - 157: 27.071 distance: 41 - 160: 18.816 distance: 44 - 173: 36.864 distance: 111 - 187: 32.058 distance: 114 - 184: 37.817 distance: 145 - 150: 30.312 distance: 150 - 151: 36.120 distance: 151 - 152: 27.306 distance: 151 - 154: 51.239 distance: 152 - 153: 41.093 distance: 154 - 155: 36.508 distance: 154 - 156: 30.644 distance: 157 - 158: 41.560 distance: 158 - 159: 54.858 distance: 158 - 161: 41.140 distance: 159 - 160: 52.195 distance: 159 - 166: 43.839 distance: 161 - 162: 44.109 distance: 162 - 163: 42.744 distance: 163 - 164: 19.418 distance: 163 - 165: 31.192 distance: 166 - 167: 28.786 distance: 167 - 168: 58.992 distance: 167 - 170: 32.275 distance: 168 - 169: 62.914 distance: 168 - 173: 69.528 distance: 170 - 171: 21.071 distance: 170 - 172: 26.759 distance: 173 - 174: 55.138 distance: 174 - 175: 69.606 distance: 174 - 177: 42.217 distance: 175 - 176: 59.708 distance: 175 - 184: 40.908 distance: 177 - 178: 22.415 distance: 178 - 179: 21.102 distance: 178 - 180: 6.013 distance: 179 - 181: 33.147 distance: 180 - 182: 21.842 distance: 181 - 183: 14.307 distance: 182 - 183: 20.485 distance: 184 - 185: 54.766 distance: 185 - 186: 56.592 distance: 185 - 188: 43.042 distance: 186 - 187: 63.494 distance: 186 - 195: 63.954 distance: 188 - 189: 25.369 distance: 189 - 190: 18.112 distance: 190 - 191: 18.773 distance: 191 - 192: 18.976 distance: 192 - 193: 12.859 distance: 192 - 194: 26.223 distance: 195 - 196: 58.077 distance: 195 - 201: 44.721 distance: 196 - 197: 60.037 distance: 196 - 199: 46.136 distance: 197 - 198: 50.794 distance: 197 - 202: 4.391 distance: 199 - 200: 31.530 distance: 200 - 201: 38.079 distance: 202 - 203: 25.348 distance: 203 - 204: 48.947 distance: 203 - 206: 27.159 distance: 204 - 205: 56.006 distance: 204 - 208: 58.148 distance: 206 - 207: 28.345 distance: 208 - 209: 45.481 distance: 209 - 210: 45.615 distance: 210 - 211: 48.745 distance: 210 - 212: 28.291 distance: 212 - 213: 20.891 distance: 213 - 214: 30.830 distance: 214 - 215: 56.112 distance: 214 - 216: 49.987 distance: 216 - 217: 55.748 distance: 217 - 218: 28.189 distance: 217 - 220: 28.217 distance: 218 - 219: 34.011 distance: 218 - 224: 5.322 distance: 220 - 221: 41.417 distance: 221 - 222: 53.677 distance: 221 - 223: 41.221