Starting phenix.real_space_refine on Sun Dec 17 00:56:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koo_22979/12_2023/7koo_22979_trim.pdb" } resolution = 3.0 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= 0.005 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 165 5.16 5 C 12210 2.51 5 N 3035 2.21 5 O 3500 1.98 5 H 18180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37095 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "G" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "I" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "N" 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: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "R" 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: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 15.54, per 1000 atoms: 0.42 Number of scatterers: 37095 At special positions: 0 Unit cell: (130.559, 129.48, 167.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 165 16.00 O 3500 8.00 N 3035 7.00 C 12210 6.00 H 18180 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 44 " distance=2.04 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 33 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 65 " distance=2.04 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 44 " distance=2.04 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 33 " distance=2.04 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 59 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 65 " distance=2.04 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 23 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 44 " distance=2.04 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 33 " distance=2.04 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 65 " distance=2.04 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 23 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 44 " distance=2.04 Simple disulfide: pdb=" SG CYS I 29 " - pdb=" SG CYS I 33 " distance=2.04 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 65 " distance=2.04 Simple disulfide: pdb=" SG CYS J 3 " - pdb=" SG CYS J 23 " distance=2.03 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 44 " distance=2.04 Simple disulfide: pdb=" SG CYS J 29 " - pdb=" SG CYS J 33 " distance=2.04 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 59 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 65 " distance=2.03 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 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG B 501 " - " ASN B 67 " " NAG C 501 " - " ASN C 67 " " NAG D 501 " - " ASN D 67 " " NAG E 501 " - " ASN E 67 " " NAG K 1 " - " ASN A 110 " " NAG L 1 " - " ASN A 23 " " NAG M 1 " - " ASN B 110 " " NAG N 1 " - " ASN B 23 " " NAG O 1 " - " ASN C 110 " " NAG P 1 " - " ASN C 23 " " NAG Q 1 " - " ASN D 110 " " NAG R 1 " - " ASN D 23 " " NAG S 1 " - " ASN E 110 " " NAG T 1 " - " ASN E 23 " Time building additional restraints: 29.33 Conformation dependent library (CDL) restraints added in 3.9 seconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.3% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.569A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.513A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.701A pdb=" N GLN C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.066A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.931A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 227 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER E 475 " --> pdb=" O VAL E 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 21.375A pdb=" N ARG A 182 " --> pdb=" O CYS F 44 " (cutoff:3.500A) removed outlier: 18.350A pdb=" N CYS F 44 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N GLU A 184 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU F 42 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE A 186 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 21.147A pdb=" N ARG B 182 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 18.147A pdb=" N CYS G 44 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLU B 184 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU G 42 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B 186 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 22 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 21.090A pdb=" N ARG C 182 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 18.140A pdb=" N CYS H 44 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N GLU C 184 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU H 42 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 186 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 22 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 21.338A pdb=" N ARG D 182 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 18.360A pdb=" N CYS I 44 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 12.052A pdb=" N GLU D 184 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LEU I 42 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE D 186 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU I 22 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 21.218A pdb=" N ARG E 182 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 18.273A pdb=" N CYS J 44 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLU E 184 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LEU J 42 " --> pdb=" O GLU E 184 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE E 186 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 22 " --> pdb=" O ALA J 45 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2940 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: 15.13 Time building geometry restraints manager: 30.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18135 1.03 - 1.23: 336 1.23 - 1.43: 7859 1.43 - 1.62: 11045 1.62 - 1.82: 220 Bond restraints: 37595 Sorted by residual: bond pdb=" C ALA E 101 " pdb=" N THR E 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA B 101 " pdb=" N THR B 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA A 101 " pdb=" N THR A 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA D 101 " pdb=" N THR D 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA C 101 " pdb=" N THR C 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.33e+01 ... (remaining 37590 not shown) Histogram of bond angle deviations from ideal: 82.59 - 92.92: 15 92.92 - 103.26: 267 103.26 - 113.60: 45146 113.60 - 123.94: 19681 123.94 - 134.28: 2736 Bond angle restraints: 67845 Sorted by residual: angle pdb=" CB LEU D 292 " pdb=" CG LEU D 292 " pdb=" HG LEU D 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU B 292 " pdb=" CG LEU B 292 " pdb=" HG LEU B 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU A 292 " pdb=" CG LEU A 292 " pdb=" HG LEU A 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU E 292 " pdb=" CG LEU E 292 " pdb=" HG LEU E 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" CB LEU C 292 " pdb=" CG LEU C 292 " pdb=" HG LEU C 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 ... (remaining 67840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16447 18.00 - 35.99: 1101 35.99 - 53.99: 270 53.99 - 71.98: 57 71.98 - 89.98: 20 Dihedral angle restraints: 17895 sinusoidal: 9650 harmonic: 8245 Sorted by residual: dihedral pdb=" CB CYS G 60 " pdb=" SG CYS G 60 " pdb=" SG CYS G 65 " pdb=" CB CYS G 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.56 -48.44 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " pdb=" SG CYS J 65 " pdb=" CB CYS J 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.58 -48.42 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS I 60 " pdb=" SG CYS I 60 " pdb=" SG CYS I 65 " pdb=" CB CYS I 65 " ideal model delta sinusoidal sigma weight residual -86.00 -37.60 -48.40 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 17892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 3080 0.347 - 0.694: 5 0.694 - 1.041: 0 1.041 - 1.388: 0 1.388 - 1.735: 5 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CG LEU C 292 " pdb=" CB LEU C 292 " pdb=" CD1 LEU C 292 " pdb=" CD2 LEU C 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 chirality pdb=" CG LEU E 292 " pdb=" CB LEU E 292 " pdb=" CD1 LEU E 292 " pdb=" CD2 LEU E 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU B 292 " pdb=" CB LEU B 292 " pdb=" CD1 LEU B 292 " pdb=" CD2 LEU B 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 ... (remaining 3087 not shown) Planarity restraints: 5420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 469 " -0.075 2.00e-02 2.50e+03 7.63e-02 8.73e+01 pdb=" CG ASN C 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN C 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN C 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.70e+01 pdb=" CG ASN B 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN B 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN B 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.69e+01 pdb=" CG ASN E 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN E 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN E 469 " 0.107 2.00e-02 2.50e+03 ... (remaining 5417 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 598 2.08 - 2.71: 60129 2.71 - 3.34: 102023 3.34 - 3.97: 131964 3.97 - 4.60: 212097 Nonbonded interactions: 506811 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O GLU E 97 " model vdw 1.447 1.850 nonbonded pdb=" OD1 ASP D 88 " pdb=" HG SER D 147 " model vdw 1.543 1.850 nonbonded pdb=" OD1 ASP A 88 " pdb=" HG SER A 147 " model vdw 1.544 1.850 nonbonded pdb=" OD1 ASP B 88 " pdb=" HG SER B 147 " model vdw 1.544 1.850 nonbonded pdb=" OD1 ASP C 88 " pdb=" HG SER C 147 " model vdw 1.544 1.850 ... (remaining 506806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 0.680 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: 0.550 Extract box with map and model: 5.390 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 114.360 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.400 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.010 0.120 19415 Z= 0.641 Angle : 1.135 17.285 26450 Z= 0.676 Chirality : 0.090 1.735 3090 Planarity : 0.007 0.043 3250 Dihedral : 13.838 89.980 7355 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.20 % Allowed : 1.44 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2285 helix: 0.55 (0.17), residues: 905 sheet: -0.78 (0.22), residues: 475 loop : -1.17 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 59 HIS 0.014 0.002 HIS E 296 PHE 0.068 0.004 PHE C 452 TYR 0.039 0.003 TYR C 187 ARG 0.024 0.002 ARG I 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 3.028 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 291 average time/residue: 1.6862 time to fit residues: 595.5285 Evaluate side-chains 199 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 2 average time/residue: 0.3828 time to fit residues: 4.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 46 ASN C 38 GLN D 38 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19415 Z= 0.194 Angle : 0.616 11.480 26450 Z= 0.309 Chirality : 0.080 1.735 3090 Planarity : 0.005 0.049 3250 Dihedral : 6.740 59.762 3010 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.77 % Allowed : 8.15 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2285 helix: 1.30 (0.17), residues: 890 sheet: -0.76 (0.20), residues: 555 loop : -0.81 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 437 HIS 0.002 0.001 HIS D 296 PHE 0.014 0.001 PHE B 99 TYR 0.012 0.001 TYR B 419 ARG 0.002 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 3.139 Fit side-chains outliers start: 37 outliers final: 10 residues processed: 223 average time/residue: 1.7137 time to fit residues: 461.8902 Evaluate side-chains 189 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 1.6437 time to fit residues: 9.3742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: