Starting phenix.real_space_refine on Tue Dec 12 00:04:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/12_2023/7xq9_33391.pdb" } resolution = 3.3 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= 0.006 sd= 0.175 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 96 5.16 5 C 13080 2.51 5 N 3120 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ASP 12": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 238": "OD1" <-> "OD2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H ASP 12": "OD1" <-> "OD2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "I ASP 3": "OD1" <-> "OD2" Residue "I ASP 12": "OD1" <-> "OD2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ASP 238": "OD1" <-> "OD2" Residue "J ASP 3": "OD1" <-> "OD2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J ASP 238": "OD1" <-> "OD2" Residue "K ASP 3": "OD1" <-> "OD2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 238": "OD1" <-> "OD2" Residue "L ASP 3": "OD1" <-> "OD2" Residue "L ASP 12": "OD1" <-> "OD2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ASP 238": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19632 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "I" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "J" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Time building chain proxies: 10.43, per 1000 atoms: 0.53 Number of scatterers: 19632 At special positions: 0 Unit cell: (106.392, 108.68, 181.896, 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 96 16.00 O 3336 8.00 N 3120 7.00 C 13080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " 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 Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 3.8 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N LYS A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 110 Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N LYS G 102 " --> pdb=" O TYR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.658A pdb=" N TYR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 236 " --> pdb=" O PHE G 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix removed outlier: 3.584A pdb=" N LYS B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix removed outlier: 3.584A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix removed outlier: 3.584A pdb=" N LYS D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N LYS E 102 " --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N LYS F 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.700A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 45' Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 110 Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N LYS H 102 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS H 206 " --> pdb=" O ARG H 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 236 " --> pdb=" O PHE H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 45' Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 110 Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N LYS I 102 " --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER I 163 " --> pdb=" O ILE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 236 " --> pdb=" O PHE I 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 110 Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N LYS J 102 " --> pdb=" O TYR J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL J 236 " --> pdb=" O PHE J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 45' Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 110 Proline residue: K 88 - end of helix removed outlier: 3.584A pdb=" N LYS K 102 " --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER K 163 " --> pdb=" O ILE K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 236 " --> pdb=" O PHE K 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 45' Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 110 Proline residue: L 88 - end of helix removed outlier: 3.584A pdb=" N LYS L 102 " --> pdb=" O TYR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.712A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 8.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5796 1.34 - 1.46: 4036 1.46 - 1.57: 10196 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 20148 Sorted by residual: bond pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.73e+00 bond pdb=" N HIS I 194 " pdb=" CA HIS I 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.67e+00 bond pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.65e+00 bond pdb=" N HIS J 194 " pdb=" CA HIS J 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.64e+00 bond pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.63e+00 ... (remaining 20143 not shown) Histogram of bond angle deviations from ideal: 100.95 - 107.56: 588 107.56 - 114.17: 11371 114.17 - 120.77: 9313 120.77 - 127.38: 5788 127.38 - 133.99: 228 Bond angle restraints: 27288 Sorted by residual: angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO K 193 " pdb=" N HIS K 194 " pdb=" CA HIS K 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO H 193 " pdb=" N HIS H 194 " pdb=" CA HIS H 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.48e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 120.79 127.71 -6.92 1.39e+00 5.18e-01 2.48e+01 ... (remaining 27283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.95: 9458 11.95 - 23.89: 1534 23.89 - 35.84: 552 35.84 - 47.78: 192 47.78 - 59.73: 72 Dihedral angle restraints: 11808 sinusoidal: 4752 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.46 -26.46 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS I 61 " pdb=" SG CYS I 61 " pdb=" SG CYS I 192 " pdb=" CB CYS I 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.45 -26.45 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS F 61 " pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " pdb=" CB CYS F 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.44 -26.44 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 11805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3012 0.113 - 0.226: 60 0.226 - 0.340: 12 0.340 - 0.453: 0 0.453 - 0.566: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB ILE D 34 " pdb=" CA ILE D 34 " pdb=" CG1 ILE D 34 " pdb=" CG2 ILE D 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3093 not shown) Planarity restraints: 3300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 12 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CG ASP I 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP I 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 12 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" CG ASP K 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP K 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP K 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 12 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" CG ASP B 12 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP B 12 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 12 " -0.010 2.00e-02 2.50e+03 ... (remaining 3297 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4595 2.78 - 3.31: 16566 3.31 - 3.84: 31244 3.84 - 4.37: 31952 4.37 - 4.90: 59471 Nonbonded interactions: 143828 Sorted by model distance: nonbonded pdb=" O ILE K 72 " pdb=" OH TYR K 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE G 72 " pdb=" OH TYR G 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE D 72 " pdb=" OH TYR D 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.253 2.440 ... (remaining 143823 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.760 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: 0.020 Extract box with map and model: 4.710 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 51.370 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 20148 Z= 0.320 Angle : 0.826 7.699 27288 Z= 0.480 Chirality : 0.057 0.566 3096 Planarity : 0.006 0.040 3300 Dihedral : 14.697 59.726 7140 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.89 % Allowed : 2.27 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.05 (0.14), residues: 2364 helix: -0.92 (0.10), residues: 1668 sheet: 1.27 (0.48), residues: 132 loop : -2.97 (0.20), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 45 HIS 0.001 0.001 HIS I 194 PHE 0.021 0.002 PHE H 212 TYR 0.011 0.001 TYR G 66 ARG 0.002 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 524 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 34 residues processed: 582 average time/residue: 0.3446 time to fit residues: 292.8801 Evaluate side-chains 455 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 421 time to evaluate : 2.450 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1650 time to fit residues: 13.8684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 194 HIS D 15 GLN H 194 HIS I 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20148 Z= 0.154 Angle : 0.478 5.858 27288 Z= 0.256 Chirality : 0.033 0.113 3096 Planarity : 0.003 0.033 3300 Dihedral : 3.834 15.770 2592 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.02 % Allowed : 10.88 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.24 (0.17), residues: 2364 helix: 1.81 (0.12), residues: 1668 sheet: 2.00 (0.49), residues: 132 loop : -2.67 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.003 0.001 HIS B 194 PHE 0.012 0.001 PHE E 169 TYR 0.012 0.001 TYR E 230 ARG 0.002 0.000 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 451 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 466 average time/residue: 0.3337 time to fit residues: 231.5775 Evaluate side-chains 430 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 419 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1454 time to fit residues: 5.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 81 GLN G 81 GLN B 81 GLN C 81 GLN D 15 GLN D 81 GLN E 81 GLN F 81 GLN I 81 GLN K 81 GLN L 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20148 Z= 0.294 Angle : 0.543 5.106 27288 Z= 0.292 Chirality : 0.036 0.129 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.630 13.447 2592 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.13 % Allowed : 12.69 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.19 (0.17), residues: 2364 helix: 2.53 (0.12), residues: 1668 sheet: 2.42 (0.48), residues: 132 loop : -2.37 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.003 0.001 HIS H 194 PHE 0.017 0.002 PHE L 169 TYR 0.011 0.001 TYR I 66 ARG 0.003 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 430 time to evaluate : 2.419 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 31 residues processed: 455 average time/residue: 0.3339 time to fit residues: 226.9447 Evaluate side-chains 436 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 405 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1732 time to fit residues: 13.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 55 ASN F 55 ASN H 55 ASN J 55 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20148 Z= 0.142 Angle : 0.440 5.423 27288 Z= 0.238 Chirality : 0.033 0.124 3096 Planarity : 0.003 0.031 3300 Dihedral : 3.417 13.452 2592 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.88 % Allowed : 15.65 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.62 (0.17), residues: 2364 helix: 2.87 (0.12), residues: 1668 sheet: 2.37 (0.47), residues: 132 loop : -2.23 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 45 HIS 0.001 0.000 HIS E 194 PHE 0.011 0.001 PHE F 229 TYR 0.014 0.001 TYR D 230 ARG 0.001 0.000 ARG J 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 446 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 450 average time/residue: 0.3329 time to fit residues: 222.8748 Evaluate side-chains 426 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 415 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1780 time to fit residues: 6.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN C 55 ASN D 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20148 Z= 0.212 Angle : 0.469 5.340 27288 Z= 0.254 Chirality : 0.034 0.124 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.300 12.698 2592 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.06 % Allowed : 17.27 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.79 (0.17), residues: 2364 helix: 2.92 (0.12), residues: 1680 sheet: 2.45 (0.47), residues: 132 loop : -2.00 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 45 HIS 0.002 0.000 HIS H 194 PHE 0.012 0.001 PHE A 32 TYR 0.010 0.001 TYR F 66 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 430 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 440 average time/residue: 0.3381 time to fit residues: 220.2228 Evaluate side-chains 434 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 418 time to evaluate : 2.299 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1781 time to fit residues: 8.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 15 GLN D 55 ASN H 55 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20148 Z= 0.167 Angle : 0.453 5.365 27288 Z= 0.246 Chirality : 0.033 0.119 3096 Planarity : 0.003 0.030 3300 Dihedral : 3.227 12.912 2592 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.69 % Allowed : 17.69 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.01 (0.17), residues: 2364 helix: 3.09 (0.12), residues: 1680 sheet: 2.36 (0.47), residues: 132 loop : -1.90 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE A 32 TYR 0.009 0.001 TYR H 175 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 447 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 453 average time/residue: 0.3664 time to fit residues: 245.2352 Evaluate side-chains 438 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 428 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1842 time to fit residues: 6.6032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 0.0370 chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN C 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20148 Z= 0.145 Angle : 0.453 7.312 27288 Z= 0.245 Chirality : 0.033 0.113 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.070 13.151 2592 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.51 % Allowed : 18.98 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.20 (0.17), residues: 2364 helix: 3.23 (0.12), residues: 1680 sheet: 2.28 (0.46), residues: 132 loop : -1.81 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 45 HIS 0.001 0.000 HIS C 95 PHE 0.011 0.001 PHE A 32 TYR 0.008 0.001 TYR A 17 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 468 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 472 average time/residue: 0.3389 time to fit residues: 235.5373 Evaluate side-chains 456 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 449 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1840 time to fit residues: 5.4536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20148 Z= 0.163 Angle : 0.471 6.597 27288 Z= 0.253 Chirality : 0.033 0.142 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.033 12.764 2592 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.23 % Allowed : 20.09 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.32 (0.17), residues: 2364 helix: 3.33 (0.12), residues: 1680 sheet: 2.26 (0.46), residues: 132 loop : -1.74 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 45 HIS 0.001 0.000 HIS I 95 PHE 0.011 0.001 PHE A 32 TYR 0.016 0.001 TYR A 230 ARG 0.001 0.000 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 452 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 453 average time/residue: 0.3537 time to fit residues: 235.2527 Evaluate side-chains 448 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 444 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1934 time to fit residues: 4.8120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN L 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20148 Z= 0.173 Angle : 0.478 6.453 27288 Z= 0.258 Chirality : 0.033 0.117 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.014 12.531 2592 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.19 % Allowed : 20.28 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.39 (0.17), residues: 2364 helix: 3.37 (0.12), residues: 1680 sheet: 2.28 (0.46), residues: 132 loop : -1.69 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 25 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE A 32 TYR 0.021 0.001 TYR G 230 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 450 average time/residue: 0.3521 time to fit residues: 232.8814 Evaluate side-chains 444 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 442 time to evaluate : 2.219 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1933 time to fit residues: 3.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0970 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 0.0030 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN E 224 ASN H 55 ASN I 224 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20148 Z= 0.149 Angle : 0.479 7.094 27288 Z= 0.258 Chirality : 0.033 0.110 3096 Planarity : 0.003 0.029 3300 Dihedral : 2.944 13.048 2592 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.28 % Allowed : 20.79 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.47 (0.17), residues: 2364 helix: 3.46 (0.12), residues: 1680 sheet: 2.20 (0.46), residues: 132 loop : -1.74 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 45 HIS 0.001 0.000 HIS A 95 PHE 0.010 0.001 PHE A 32 TYR 0.009 0.001 TYR B 17 ARG 0.003 0.000 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 467 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 468 average time/residue: 0.3425 time to fit residues: 236.5744 Evaluate side-chains 462 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 459 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1712 time to fit residues: 4.1587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100812 restraints weight = 28705.900| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.52 r_work: 0.3132 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20148 Z= 0.148 Angle : 0.467 6.744 27288 Z= 0.252 Chirality : 0.033 0.113 3096 Planarity : 0.003 0.028 3300 Dihedral : 2.892 12.964 2592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.09 % Allowed : 20.79 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.52 (0.17), residues: 2364 helix: 3.49 (0.12), residues: 1680 sheet: 2.23 (0.46), residues: 132 loop : -1.72 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 45 HIS 0.001 0.000 HIS K 95 PHE 0.010 0.001 PHE A 32 TYR 0.021 0.001 TYR J 230 ARG 0.001 0.000 ARG D 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.87 seconds wall clock time: 86 minutes 50.78 seconds (5210.78 seconds total)