Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 07:54:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qd7_4520/04_2023/6qd7_4520_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.103 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 51 5.16 5 C 9123 2.51 5 N 2466 2.21 5 O 2805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ASP 591": "OD1" <-> "OD2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B ASP 621": "OD1" <-> "OD2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ASP 192": "OD1" <-> "OD2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "D ASP 522": "OD1" <-> "OD2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 540": "OE1" <-> "OE2" Residue "D ASP 552": "OD1" <-> "OD2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ASP 591": "OD1" <-> "OD2" Residue "D ASP 607": "OD1" <-> "OD2" Residue "D ASP 621": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "F ASP 522": "OD1" <-> "OD2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 540": "OE1" <-> "OE2" Residue "F ASP 552": "OD1" <-> "OD2" Residue "F ARG 559": "NH1" <-> "NH2" Residue "F GLU 578": "OE1" <-> "OE2" Residue "F ASP 591": "OD1" <-> "OD2" Residue "F ASP 607": "OD1" <-> "OD2" Residue "F ASP 621": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 629": "OD1" <-> "OD2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 6": "OE1" <-> "OE2" Residue "U GLU 23": "OE1" <-> "OE2" Residue "U PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1": "OE1" <-> "OE2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14445 Number of models: 1 Model: "" Number of chains: 21 Chain: "L" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "H" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "X" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "U" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "Z" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "P" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "G" 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 chiralities: 4 Chain: "I" 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 chiralities: 4 Chain: "J" 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 chiralities: 4 Chain: "A" 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 chiralities: 1 Chain: "B" 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 chiralities: 1 Chain: "C" 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 chiralities: 1 Chain: "E" 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 chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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 chiralities: 1 Time building chain proxies: 8.67, per 1000 atoms: 0.60 Number of scatterers: 14445 At special positions: 0 Unit cell: (133.45, 123.25, 126.65, 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 51 16.00 O 2805 8.00 N 2466 7.00 C 9123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.05 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.01 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.20 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.90 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 93 " distance=2.05 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 93 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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 ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 701 " - " ASN B 618 " " NAG D 701 " - " ASN D 618 " " NAG F 701 " - " ASN F 618 " " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 2.6 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 36 sheets defined 16.2% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.676A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 551 through 575 removed outlier: 5.966A pdb=" N ILE B 555 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 557 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 559 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 567 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 613 through 621 Processing helix chain 'B' and resid 624 through 627 No H-bonds generated for 'chain 'B' and resid 624 through 627' Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.676A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 79 through 85 removed outlier: 3.676A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'D' and resid 539 through 541 No H-bonds generated for 'chain 'D' and resid 539 through 541' Processing helix chain 'D' and resid 551 through 575 removed outlier: 5.966A pdb=" N ILE D 555 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 557 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 559 " --> pdb=" O CYS D 556 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN D 567 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 597 Processing helix chain 'D' and resid 613 through 621 Processing helix chain 'D' and resid 624 through 627 No H-bonds generated for 'chain 'D' and resid 624 through 627' Processing helix chain 'F' and resid 539 through 541 No H-bonds generated for 'chain 'F' and resid 539 through 541' Processing helix chain 'F' and resid 551 through 575 removed outlier: 5.967A pdb=" N ILE F 555 " --> pdb=" O ASP F 552 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 557 " --> pdb=" O LEU F 554 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG F 559 " --> pdb=" O CYS F 556 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN F 567 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 613 through 621 Processing helix chain 'F' and resid 624 through 627 No H-bonds generated for 'chain 'F' and resid 624 through 627' Processing helix chain 'X' and resid 29 through 31 No H-bonds generated for 'chain 'X' and resid 29 through 31' Processing helix chain 'X' and resid 62 through 64 No H-bonds generated for 'chain 'X' and resid 62 through 64' Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'X' and resid 85 through 87 No H-bonds generated for 'chain 'X' and resid 85 through 87' Processing helix chain 'U' and resid 29 through 31 No H-bonds generated for 'chain 'U' and resid 29 through 31' Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 85 through 87 No H-bonds generated for 'chain 'U' and resid 85 through 87' Processing helix chain 'Z' and resid 80 through 82 No H-bonds generated for 'chain 'Z' and resid 80 through 82' Processing helix chain 'P' and resid 80 through 82 No H-bonds generated for 'chain 'P' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.166A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU L 105 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.972A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 94 through 96 removed outlier: 3.927A pdb=" N LEU H 107 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= G, first strand: chain 'A' and resid 63 through 69 Processing sheet with id= H, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= I, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= J, first strand: chain 'A' and resid 107 through 114 removed outlier: 6.509A pdb=" N TYR A 137 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN A 110 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS A 139 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU A 112 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 141 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS A 114 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 143 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR A 216 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS A 140 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 218 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 142 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 220 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR A 144 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA A 222 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 232 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU A 273 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN A 243 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TRP A 275 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 306 through 309 Processing sheet with id= L, first strand: chain 'B' and resid 515 through 520 Processing sheet with id= M, first strand: chain 'C' and resid 36 through 39 Processing sheet with id= N, first strand: chain 'C' and resid 63 through 69 Processing sheet with id= O, first strand: chain 'C' and resid 86 through 89 Processing sheet with id= P, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= Q, first strand: chain 'C' and resid 107 through 114 removed outlier: 6.510A pdb=" N TYR C 137 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN C 110 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS C 139 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU C 112 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 141 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C 114 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY C 143 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C 216 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 140 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 218 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 142 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR C 220 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR C 144 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA C 222 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR C 232 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU C 273 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN C 243 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TRP C 275 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 306 through 309 Processing sheet with id= S, first strand: chain 'E' and resid 36 through 39 Processing sheet with id= T, first strand: chain 'E' and resid 63 through 69 Processing sheet with id= U, first strand: chain 'E' and resid 86 through 89 Processing sheet with id= V, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= W, first strand: chain 'E' and resid 107 through 114 removed outlier: 6.509A pdb=" N TYR E 137 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN E 110 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS E 139 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLU E 112 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL E 141 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS E 114 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY E 143 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR E 216 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS E 140 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 218 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER E 142 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR E 220 " --> pdb=" O SER E 142 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR E 144 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA E 222 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR E 232 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU E 273 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN E 243 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TRP E 275 " --> pdb=" O GLN E 243 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 306 through 309 Processing sheet with id= Y, first strand: chain 'D' and resid 515 through 520 Processing sheet with id= Z, first strand: chain 'F' and resid 515 through 520 Processing sheet with id= AA, first strand: chain 'X' and resid 3 through 7 Processing sheet with id= AB, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.972A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 94 through 96 removed outlier: 3.927A pdb=" N LEU X 107 " --> pdb=" O LYS X 95 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 3 through 7 Processing sheet with id= AE, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.973A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 94 through 96 removed outlier: 3.927A pdb=" N LEU U 107 " --> pdb=" O LYS U 95 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id= AH, first strand: chain 'Z' and resid 10 through 13 removed outlier: 7.099A pdb=" N LYS Z 103 " --> pdb=" O LEU Z 11 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU Z 13 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU Z 105 " --> pdb=" O LEU Z 13 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Z 84 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN Z 37 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU Z 46 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'P' and resid 4 through 7 Processing sheet with id= AJ, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.862A pdb=" N LYS P 103 " --> pdb=" O LEU P 11 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU P 13 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU P 105 " --> pdb=" O LEU P 13 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1023 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: 4.58 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4220 1.34 - 1.46: 3679 1.46 - 1.59: 6807 1.59 - 1.71: 3 1.71 - 1.83: 60 Bond restraints: 14769 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C5 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 14764 not shown) Histogram of bond angle deviations from ideal: 99.98 - 107.67: 894 107.67 - 115.36: 8271 115.36 - 123.04: 9226 123.04 - 130.73: 1601 130.73 - 138.42: 84 Bond angle restraints: 20076 Sorted by residual: angle pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " pdb=" CG LEU A 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU E 256 " pdb=" CB LEU E 256 " pdb=" CG LEU E 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU C 256 " pdb=" CB LEU C 256 " pdb=" CG LEU C 256 " ideal model delta sigma weight residual 116.30 137.48 -21.18 3.50e+00 8.16e-02 3.66e+01 angle pdb=" CA GLU A 229 " pdb=" CB GLU A 229 " pdb=" CG GLU A 229 " ideal model delta sigma weight residual 114.10 125.69 -11.59 2.00e+00 2.50e-01 3.36e+01 angle pdb=" CA GLU C 229 " pdb=" CB GLU C 229 " pdb=" CG GLU C 229 " ideal model delta sigma weight residual 114.10 125.65 -11.55 2.00e+00 2.50e-01 3.34e+01 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 7878 17.16 - 34.33: 549 34.33 - 51.49: 143 51.49 - 68.65: 41 68.65 - 85.81: 29 Dihedral angle restraints: 8640 sinusoidal: 3375 harmonic: 5265 Sorted by residual: dihedral pdb=" C ASN F 618 " pdb=" N ASN F 618 " pdb=" CA ASN F 618 " pdb=" CB ASN F 618 " ideal model delta harmonic sigma weight residual -122.60 -135.12 12.52 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ASN B 618 " pdb=" N ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ASN D 618 " pdb=" N ASN D 618 " pdb=" CA ASN D 618 " pdb=" CB ASN D 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1784 0.097 - 0.193: 423 0.193 - 0.290: 56 0.290 - 0.387: 13 0.387 - 0.483: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CB ILE E 274 " pdb=" CA ILE E 274 " pdb=" CG1 ILE E 274 " pdb=" CG2 ILE E 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE A 274 " pdb=" CA ILE A 274 " pdb=" CG1 ILE A 274 " pdb=" CG2 ILE A 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB ILE C 274 " pdb=" CA ILE C 274 " pdb=" CG1 ILE C 274 " pdb=" CG2 ILE C 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2283 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.044 2.00e-02 2.50e+03 8.66e-02 7.49e+01 pdb=" CD GLU E 235 " -0.150 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.058 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " -0.044 2.00e-02 2.50e+03 8.64e-02 7.47e+01 pdb=" CD GLU A 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " -0.044 2.00e-02 2.50e+03 8.63e-02 7.44e+01 pdb=" CD GLU C 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " -0.048 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1947 2.77 - 3.30: 12989 3.30 - 3.83: 23223 3.83 - 4.37: 27459 4.37 - 4.90: 47588 Nonbonded interactions: 113206 Sorted by model distance: nonbonded pdb=" OD2 ASP C 78 " pdb=" OG SER C 246 " model vdw 2.233 2.440 nonbonded pdb=" OD2 ASP E 78 " pdb=" OG SER E 246 " model vdw 2.233 2.440 nonbonded pdb=" OD2 ASP A 78 " pdb=" OG SER A 246 " model vdw 2.234 2.440 nonbonded pdb=" NZ LYS F 622 " pdb=" O7 NAG F 701 " model vdw 2.310 2.520 nonbonded pdb=" NZ LYS B 622 " pdb=" O7 NAG B 701 " model vdw 2.310 2.520 ... (remaining 113201 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'U' selection = chain 'X' } ncs_group { reference = (chain 'L' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'P' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'Z' and (resid 1 through 21 or resid 23 through 108)) } 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=0.49 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.440 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 39.680 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 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 : 0.009 0.116 14769 Z= 0.561 Angle : 1.615 21.233 20076 Z= 0.868 Chirality : 0.088 0.483 2286 Planarity : 0.010 0.087 2574 Dihedral : 14.571 85.814 5205 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.11 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 9.68 % 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: -0.85 (0.18), residues: 1782 helix: 0.20 (0.30), residues: 210 sheet: -0.42 (0.20), residues: 549 loop : -0.76 (0.18), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 192 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 31 residues processed: 252 average time/residue: 0.3153 time to fit residues: 110.4166 Evaluate side-chains 161 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1285 time to fit residues: 9.7504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN A 61 ASN A 257 ASN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 257 ASN E 61 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 567 GLN F 595 GLN X 82 GLN U 82 GLN P 38 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14769 Z= 0.258 Angle : 0.750 9.430 20076 Z= 0.384 Chirality : 0.050 0.361 2286 Planarity : 0.006 0.090 2574 Dihedral : 5.433 29.142 1992 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.22 (0.19), residues: 1782 helix: 0.51 (0.34), residues: 210 sheet: -0.23 (0.21), residues: 537 loop : -0.14 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.544 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 165 average time/residue: 0.3486 time to fit residues: 79.2928 Evaluate side-chains 131 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1307 time to fit residues: 4.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Z 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14769 Z= 0.271 Angle : 0.699 8.632 20076 Z= 0.354 Chirality : 0.048 0.249 2286 Planarity : 0.006 0.064 2574 Dihedral : 5.202 34.091 1992 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1782 helix: 0.13 (0.34), residues: 210 sheet: -0.29 (0.22), residues: 504 loop : -0.43 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.561 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 168 average time/residue: 0.3271 time to fit residues: 76.7265 Evaluate side-chains 144 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1345 time to fit residues: 7.2268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 GLN Z 37 GLN P 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 14769 Z= 0.449 Angle : 0.823 9.250 20076 Z= 0.410 Chirality : 0.051 0.330 2286 Planarity : 0.007 0.075 2574 Dihedral : 5.535 23.111 1992 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1782 helix: -0.23 (0.33), residues: 228 sheet: -0.48 (0.22), residues: 519 loop : -0.93 (0.18), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 175 average time/residue: 0.3339 time to fit residues: 81.4360 Evaluate side-chains 154 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1953 time to fit residues: 9.3407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN X 110 GLN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14769 Z= 0.285 Angle : 0.682 8.937 20076 Z= 0.343 Chirality : 0.047 0.274 2286 Planarity : 0.006 0.062 2574 Dihedral : 5.182 20.649 1992 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), residues: 1782 helix: -0.14 (0.34), residues: 228 sheet: -0.59 (0.22), residues: 516 loop : -0.95 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 165 average time/residue: 0.3187 time to fit residues: 74.0041 Evaluate side-chains 157 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1642 time to fit residues: 8.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 174 optimal weight: 0.9980 chunk 144 optimal weight: 0.0770 chunk 80 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.0870 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14769 Z= 0.181 Angle : 0.617 9.051 20076 Z= 0.310 Chirality : 0.045 0.450 2286 Planarity : 0.005 0.046 2574 Dihedral : 4.891 20.913 1992 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.97 (0.19), residues: 1782 helix: -0.15 (0.34), residues: 228 sheet: -0.34 (0.22), residues: 507 loop : -0.89 (0.18), residues: 1047 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 164 average time/residue: 0.3286 time to fit residues: 76.5164 Evaluate side-chains 140 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1361 time to fit residues: 3.7463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.0070 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 0.0770 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 0.0020 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 overall best weight: 0.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 14769 Z= 0.144 Angle : 0.576 8.742 20076 Z= 0.290 Chirality : 0.044 0.467 2286 Planarity : 0.005 0.038 2574 Dihedral : 4.505 19.184 1992 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.81 (0.19), residues: 1782 helix: -0.06 (0.35), residues: 210 sheet: -0.15 (0.22), residues: 495 loop : -0.80 (0.18), residues: 1077 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.3243 time to fit residues: 71.3269 Evaluate side-chains 136 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1257 time to fit residues: 4.1732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 50.0000 chunk 69 optimal weight: 0.0270 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14769 Z= 0.329 Angle : 0.698 9.281 20076 Z= 0.347 Chirality : 0.047 0.352 2286 Planarity : 0.005 0.051 2574 Dihedral : 4.974 27.862 1992 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 1782 helix: -0.16 (0.34), residues: 228 sheet: -0.29 (0.21), residues: 567 loop : -1.01 (0.19), residues: 987 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 158 average time/residue: 0.3039 time to fit residues: 69.0494 Evaluate side-chains 145 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1385 time to fit residues: 3.8273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.3980 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 0.5980 chunk 161 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 146 optimal weight: 0.1980 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 40.0000 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 14769 Z= 0.143 Angle : 0.572 9.023 20076 Z= 0.289 Chirality : 0.044 0.291 2286 Planarity : 0.005 0.037 2574 Dihedral : 4.577 26.407 1992 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.86 (0.19), residues: 1782 helix: -0.22 (0.34), residues: 228 sheet: 0.07 (0.23), residues: 507 loop : -0.97 (0.18), residues: 1047 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 149 average time/residue: 0.3379 time to fit residues: 70.9840 Evaluate side-chains 134 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2878 time to fit residues: 3.1394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 81 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 586 ASN U 54 ASN ** Z 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 14769 Z= 0.320 Angle : 0.702 9.369 20076 Z= 0.351 Chirality : 0.047 0.273 2286 Planarity : 0.005 0.041 2574 Dihedral : 4.996 33.948 1992 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.19), residues: 1782 helix: 0.15 (0.36), residues: 210 sheet: 0.11 (0.23), residues: 504 loop : -1.06 (0.18), residues: 1068 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 148 average time/residue: 0.3266 time to fit residues: 68.9461 Evaluate side-chains 143 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1334 time to fit residues: 3.1788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 586 ASN ** Z 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.226050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175298 restraints weight = 27167.723| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 5.53 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14769 Z= 0.246 Angle : 0.643 9.455 20076 Z= 0.322 Chirality : 0.046 0.255 2286 Planarity : 0.005 0.042 2574 Dihedral : 4.879 31.323 1992 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.19), residues: 1782 helix: -0.23 (0.34), residues: 228 sheet: 0.13 (0.24), residues: 480 loop : -1.15 (0.18), residues: 1074 =============================================================================== Job complete usr+sys time: 2896.99 seconds wall clock time: 53 minutes 39.22 seconds (3219.22 seconds total)