Starting phenix.real_space_refine on Thu Feb 22 01:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac5_15334/02_2024/8ac5_15334_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21022 2.51 5 N 5294 2.21 5 O 6071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32527 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 452 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'CDL': 2, 'HEC': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 129 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'FES': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 250 Unusual residues: {'CDL': 1, 'HEC': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.132 49.735 34.434 1.00153.46 S ATOM 4207 SG CYS P 187 32.693 47.027 33.382 1.00159.22 S Time building chain proxies: 19.69, per 1000 atoms: 0.61 Number of scatterers: 32527 At special positions: 0 Unit cell: (119.691, 129.735, 164.889, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6071 8.00 N 5294 7.00 C 21022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.06 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.61 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7482 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 28 through 52 removed outlier: 3.965A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.762A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.196A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.608A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 173 through 203 Proline residue: C 187 - end of helix removed outlier: 4.104A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.892A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 273 through 284 Proline residue: C 277 - end of helix Processing helix chain 'C' and resid 288 through 308 removed outlier: 3.821A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 320 through 340 Processing helix chain 'C' and resid 348 through 364 removed outlier: 4.099A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 382 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.617A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.671A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.606A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.534A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.871A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.814A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 4.000A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.550A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.502A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.955A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.644A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.576A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.660A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.658A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.692A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.687A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.579A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 40 through 81 removed outlier: 4.370A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 44 Processing helix chain 'I' and resid 50 through 56 removed outlier: 5.134A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.572A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'N' and resid 3 through 6 No H-bonds generated for 'chain 'N' and resid 3 through 6' Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 28 through 52 removed outlier: 3.950A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 75 through 102 removed outlier: 3.758A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.515A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.628A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 166 Processing helix chain 'N' and resid 173 through 203 Proline residue: N 187 - end of helix removed outlier: 4.123A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.855A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 257 Processing helix chain 'N' and resid 273 through 284 Proline residue: N 277 - end of helix Processing helix chain 'N' and resid 288 through 308 removed outlier: 3.839A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU N 305 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Proline residue: N 306 - end of helix Processing helix chain 'N' and resid 320 through 340 Processing helix chain 'N' and resid 348 through 364 removed outlier: 4.092A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 382 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.640A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 35 Proline residue: R 26 - end of helix Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 53 through 61 Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.678A pdb=" N ASN R 121 " --> pdb=" O ASP R 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 92 through 110 Processing helix chain 'Q' and resid 124 through 137 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.619A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.873A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.814A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.992A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.507A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.946A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.655A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.671A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 413 Processing helix chain 'L' and resid 420 through 428 Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 462 through 469 removed outlier: 3.658A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET L 469 " --> pdb=" O ILE L 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 70 through 79 Processing helix chain 'M' and resid 101 through 117 Proline residue: M 105 - end of helix removed outlier: 3.652A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.695A pdb=" N LEU M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 282 No H-bonds generated for 'chain 'M' and resid 280 through 282' Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 334 through 353 Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.922A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 No H-bonds generated for 'chain 'O' and resid 135 through 138' Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.596A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 40 through 81 removed outlier: 4.367A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 5.149A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.644A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 67 through 71 Processing helix chain 'U' and resid 77 through 79 No H-bonds generated for 'chain 'U' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'C' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'P' and resid 103 through 106 Processing sheet with id= C, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.852A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.154A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.632A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 156 through 158 Processing sheet with id= J, first strand: chain 'N' and resid 21 through 23 Processing sheet with id= K, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= L, first strand: chain 'L' and resid 266 through 271 Processing sheet with id= M, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.142A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 231 through 235 removed outlier: 3.608A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 156 through 158 1584 hydrogen bonds defined for protein. 4329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.33 Time building geometry restraints manager: 15.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13461 1.40 - 1.61: 19671 1.61 - 1.82: 172 1.82 - 2.03: 30 2.03 - 2.24: 20 Bond restraints: 33354 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.297 0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sigma weight residual 1.544 1.307 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.307 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sigma weight residual 1.544 1.310 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" CAB HEC N 501 " pdb=" CBB HEC N 501 " ideal model delta sigma weight residual 1.544 1.314 0.230 2.00e-02 2.50e+03 1.33e+02 ... (remaining 33349 not shown) Histogram of bond angle deviations from ideal: 83.33 - 102.60: 382 102.60 - 121.87: 37912 121.87 - 141.13: 7028 141.13 - 160.40: 0 160.40 - 179.66: 12 Bond angle restraints: 45334 Sorted by residual: angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 96.26 15.01 1.47e+00 4.63e-01 1.04e+02 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 90.56 21.44 2.20e+00 2.07e-01 9.50e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 97.55 13.72 1.47e+00 4.63e-01 8.71e+01 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 94.03 10.30 1.14e+00 7.69e-01 8.16e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 92.60 19.40 2.20e+00 2.07e-01 7.78e+01 ... (remaining 45329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 18827 32.05 - 64.10: 1016 64.10 - 96.15: 108 96.15 - 128.20: 1 128.20 - 160.25: 3 Dihedral angle restraints: 19955 sinusoidal: 8342 harmonic: 11613 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C2B HEC C 502 " pdb=" C3B HEC C 502 " pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sinusoidal sigma weight residual 60.00 -21.70 81.70 2 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" C2B HEC N 502 " pdb=" C3B HEC N 502 " pdb=" CAB HEC N 502 " pdb=" CBB HEC N 502 " ideal model delta sinusoidal sigma weight residual 60.00 -19.86 79.86 2 1.00e+01 1.00e-02 4.65e+01 ... (remaining 19952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4344 0.174 - 0.347: 580 0.347 - 0.521: 29 0.521 - 0.695: 2 0.695 - 0.868: 4 Chirality restraints: 4959 Sorted by residual: chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.71 -0.87 2.00e-01 2.50e+01 1.89e+01 chirality pdb=" CB4 CDL D 402 " pdb=" CB3 CDL D 402 " pdb=" CB6 CDL D 402 " pdb=" OB6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.74 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.77 -0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 4956 not shown) Planarity restraints: 5698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " -0.032 2.00e-02 2.50e+03 3.27e-02 2.41e+01 pdb=" C2C HEC C 502 " -0.009 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " -0.033 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " 0.023 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " 0.058 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " 0.042 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " 0.003 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC C 502 " 0.026 2.00e-02 2.50e+03 3.14e-02 2.22e+01 pdb=" C1B HEC C 502 " 0.020 2.00e-02 2.50e+03 pdb=" C2B HEC C 502 " 0.018 2.00e-02 2.50e+03 pdb=" C3B HEC C 502 " 0.023 2.00e-02 2.50e+03 pdb=" C4B HEC C 502 " 0.041 2.00e-02 2.50e+03 pdb=" CAB HEC C 502 " -0.022 2.00e-02 2.50e+03 pdb=" CHB HEC C 502 " -0.049 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " -0.049 2.00e-02 2.50e+03 pdb=" CMB HEC C 502 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 502 " 0.024 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" C2C HEC N 502 " 0.005 2.00e-02 2.50e+03 pdb=" C3C HEC N 502 " 0.023 2.00e-02 2.50e+03 pdb=" C4C HEC N 502 " 0.020 2.00e-02 2.50e+03 pdb=" CAC HEC N 502 " -0.014 2.00e-02 2.50e+03 pdb=" CHC HEC N 502 " -0.051 2.00e-02 2.50e+03 pdb=" CHD HEC N 502 " -0.045 2.00e-02 2.50e+03 pdb=" CMC HEC N 502 " -0.002 2.00e-02 2.50e+03 pdb=" NC HEC N 502 " 0.041 2.00e-02 2.50e+03 ... (remaining 5695 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 278 2.63 - 3.20: 28891 3.20 - 3.77: 53534 3.77 - 4.33: 78388 4.33 - 4.90: 120715 Nonbonded interactions: 281806 Sorted by model distance: nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEC C 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEC N 501 " model vdw 2.071 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.078 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEC N 502 " model vdw 2.221 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEC C 502 " model vdw 2.236 3.080 ... (remaining 281801 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 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 503 or resid 506)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503 or resid 506)) } ncs_group { reference = (chain 'D' and (resid 85 through 328 or resid 401)) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = (chain 'U' and resid 8 through 82) } 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: 4.500 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: 0.030 Extract box with map and model: 12.140 Check model and map are aligned: 0.490 Set scattering table: 0.340 Process input model: 92.720 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.280 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 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 : 0.011 0.247 33354 Z= 0.715 Angle : 1.770 21.441 45334 Z= 1.097 Chirality : 0.116 0.868 4959 Planarity : 0.007 0.060 5698 Dihedral : 18.463 160.250 12458 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.61 % Allowed : 7.28 % Favored : 89.11 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 2.84 % 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: -1.30 (0.12), residues: 3953 helix: -0.99 (0.09), residues: 2118 sheet: 0.06 (0.25), residues: 359 loop : -0.62 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.007 TRP A 474 HIS 0.022 0.005 HIS N 96 PHE 0.050 0.007 PHE C 234 TYR 0.050 0.008 TYR O 177 ARG 0.021 0.002 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 411 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9202 (m) REVERT: C 239 MET cc_start: 0.9073 (ttp) cc_final: 0.8421 (mmt) REVERT: P 104 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8722 (tp30) REVERT: P 119 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7482 (tttt) REVERT: P 158 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7706 (mtpp) REVERT: P 178 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7329 (mp0) REVERT: G 97 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8785 (mt-10) REVERT: G 112 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8880 (mt-10) REVERT: F 84 GLU cc_start: 0.9140 (tt0) cc_final: 0.8846 (tp30) REVERT: F 107 LYS cc_start: 0.9349 (tttt) cc_final: 0.9090 (tmmt) REVERT: F 114 TYR cc_start: 0.8438 (t80) cc_final: 0.8235 (t80) REVERT: F 119 TYR cc_start: 0.9060 (t80) cc_final: 0.8722 (t80) REVERT: F 137 ASN cc_start: 0.9206 (m-40) cc_final: 0.8962 (m-40) REVERT: A 87 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: A 97 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9152 (mm-30) REVERT: B 134 GLU cc_start: 0.9248 (tt0) cc_final: 0.9024 (tp30) REVERT: B 345 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9030 (ttmt) REVERT: B 372 ARG cc_start: 0.8490 (ptt-90) cc_final: 0.8181 (ptt90) REVERT: B 373 ILE cc_start: 0.9309 (mm) cc_final: 0.9020 (tt) REVERT: D 85 MET cc_start: 0.8836 (mtt) cc_final: 0.8585 (mtp) REVERT: H 78 GLU cc_start: 0.9352 (tt0) cc_final: 0.9126 (pp20) REVERT: J 55 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8533 (ttm-80) REVERT: N 255 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9227 (m-30) REVERT: E 55 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8347 (p0) REVERT: R 29 LYS cc_start: 0.9345 (mttt) cc_final: 0.9137 (mmtt) REVERT: Q 77 ASP cc_start: 0.9041 (t0) cc_final: 0.8782 (t0) REVERT: Q 113 ASP cc_start: 0.9331 (m-30) cc_final: 0.8725 (t0) REVERT: M 236 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8616 (mtt180) REVERT: M 309 ASP cc_start: 0.9330 (m-30) cc_final: 0.9019 (p0) REVERT: M 341 TYR cc_start: 0.9136 (t80) cc_final: 0.8932 (t80) REVERT: M 356 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8886 (t0) REVERT: M 377 ASN cc_start: 0.9324 (m-40) cc_final: 0.8793 (m110) REVERT: O 291 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9139 (tttt) REVERT: S 78 GLU cc_start: 0.9313 (tt0) cc_final: 0.9069 (tp30) REVERT: T 7 PHE cc_start: 0.8960 (t80) cc_final: 0.8623 (m-80) REVERT: U 51 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8865 (tm-30) REVERT: U 69 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9067 (mp0) outliers start: 120 outliers final: 21 residues processed: 487 average time/residue: 0.5032 time to fit residues: 375.1838 Evaluate side-chains 292 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 0.0870 chunk 355 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 85 GLN P 90 ASN P 157 GLN G 84 HIS A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN D 93 HIS N 14 ASN N 22 GLN N 202 HIS N 332 ASN E 85 GLN E 90 ASN R 84 HIS L 332 ASN L 371 ASN M 87 HIS M 215 GLN M 241 ASN U 58 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33354 Z= 0.193 Angle : 0.608 15.292 45334 Z= 0.295 Chirality : 0.041 0.174 4959 Planarity : 0.004 0.036 5698 Dihedral : 14.256 155.732 5340 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.65 % Allowed : 9.06 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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 (0.13), residues: 3953 helix: 0.99 (0.11), residues: 2099 sheet: 0.57 (0.27), residues: 368 loop : 0.13 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 156 HIS 0.007 0.001 HIS C 197 PHE 0.020 0.001 PHE A 334 TYR 0.017 0.001 TYR D 237 ARG 0.006 0.001 ARG M 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.8996 (ttp) cc_final: 0.8315 (mmt) REVERT: C 282 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8834 (tp) REVERT: P 62 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8734 (mtm110) REVERT: P 140 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7593 (pt0) REVERT: P 178 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7281 (mp0) REVERT: G 97 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8783 (mt-10) REVERT: G 112 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: F 137 ASN cc_start: 0.8914 (m-40) cc_final: 0.8602 (m-40) REVERT: A 97 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9189 (mm-30) REVERT: B 134 GLU cc_start: 0.9132 (tt0) cc_final: 0.8866 (tp30) REVERT: B 372 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8179 (ptm-80) REVERT: B 373 ILE cc_start: 0.9301 (mm) cc_final: 0.9030 (tt) REVERT: H 78 GLU cc_start: 0.9362 (tt0) cc_final: 0.9053 (pp20) REVERT: J 15 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9146 (ptpp) REVERT: J 55 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8553 (ttm-80) REVERT: N 255 ASP cc_start: 0.9495 (OUTLIER) cc_final: 0.9123 (m-30) REVERT: E 55 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8195 (p0) REVERT: R 29 LYS cc_start: 0.9300 (mttt) cc_final: 0.9080 (mmtt) REVERT: Q 113 ASP cc_start: 0.9290 (m-30) cc_final: 0.8758 (t0) REVERT: M 309 ASP cc_start: 0.9228 (m-30) cc_final: 0.9008 (p0) REVERT: S 51 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7011 (ptm160) REVERT: S 78 GLU cc_start: 0.9334 (tt0) cc_final: 0.8993 (tp30) REVERT: U 51 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8854 (tm-30) REVERT: U 69 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8907 (pp20) outliers start: 55 outliers final: 21 residues processed: 319 average time/residue: 0.4550 time to fit residues: 233.7407 Evaluate side-chains 263 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 355 optimal weight: 30.0000 chunk 384 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 285 optimal weight: 0.4980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN M 316 GLN U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33354 Z= 0.311 Angle : 0.586 15.715 45334 Z= 0.279 Chirality : 0.042 0.170 4959 Planarity : 0.004 0.041 5698 Dihedral : 13.004 148.474 5293 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.53 % Allowed : 10.05 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.43 (0.14), residues: 3953 helix: 1.50 (0.11), residues: 2105 sheet: 0.64 (0.27), residues: 367 loop : 0.39 (0.17), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 142 HIS 0.013 0.001 HIS C 197 PHE 0.017 0.002 PHE A 334 TYR 0.024 0.002 TYR F 119 ARG 0.003 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9047 (ttp) cc_final: 0.8361 (mmt) REVERT: C 282 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8949 (tp) REVERT: P 62 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8831 (mtm110) REVERT: P 104 GLU cc_start: 0.8364 (tp30) cc_final: 0.8135 (tp30) REVERT: P 130 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7085 (ttp-170) REVERT: P 164 MET cc_start: 0.8853 (mpp) cc_final: 0.8624 (mpp) REVERT: P 196 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7729 (tp) REVERT: G 112 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8978 (tm-30) REVERT: F 107 LYS cc_start: 0.9079 (tmmt) cc_final: 0.8775 (tmmt) REVERT: A 94 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8712 (mp) REVERT: A 97 GLU cc_start: 0.9463 (OUTLIER) cc_final: 0.9071 (mm-30) REVERT: B 134 GLU cc_start: 0.9165 (tt0) cc_final: 0.8909 (tp30) REVERT: B 168 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8395 (mt0) REVERT: B 373 ILE cc_start: 0.9332 (mm) cc_final: 0.9046 (tp) REVERT: H 78 GLU cc_start: 0.9414 (tt0) cc_final: 0.9139 (tm-30) REVERT: N 255 ASP cc_start: 0.9518 (OUTLIER) cc_final: 0.9152 (m-30) REVERT: E 55 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8234 (p0) REVERT: R 29 LYS cc_start: 0.9316 (mttt) cc_final: 0.9069 (mmtt) REVERT: Q 113 ASP cc_start: 0.9339 (m-30) cc_final: 0.8780 (t0) REVERT: M 309 ASP cc_start: 0.9260 (m-30) cc_final: 0.8986 (p0) REVERT: S 51 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.6962 (ptm-80) REVERT: S 78 GLU cc_start: 0.9370 (tt0) cc_final: 0.9058 (tp30) REVERT: U 51 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8959 (tm-30) outliers start: 51 outliers final: 25 residues processed: 288 average time/residue: 0.4583 time to fit residues: 213.5012 Evaluate side-chains 269 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 356 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 132 HIS A 364 HIS R 39 GLN R 56 GLN L 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33354 Z= 0.309 Angle : 0.571 16.098 45334 Z= 0.266 Chirality : 0.042 0.146 4959 Planarity : 0.004 0.044 5698 Dihedral : 12.538 148.557 5285 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.38 % Allowed : 10.74 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.57 (0.14), residues: 3953 helix: 1.60 (0.11), residues: 2120 sheet: 0.72 (0.27), residues: 369 loop : 0.45 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.027 0.002 TYR F 114 ARG 0.005 0.000 ARG U 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9036 (ttp) cc_final: 0.8350 (mmt) REVERT: C 282 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8997 (tp) REVERT: P 62 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8828 (mtm110) REVERT: P 130 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.7084 (ttp-170) REVERT: P 158 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7995 (ttmm) REVERT: P 196 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7640 (tp) REVERT: G 112 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9039 (tm-30) REVERT: A 94 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8721 (mm) REVERT: A 97 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.9047 (mm-30) REVERT: B 134 GLU cc_start: 0.9167 (tt0) cc_final: 0.8926 (tp30) REVERT: B 168 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: B 373 ILE cc_start: 0.9338 (mm) cc_final: 0.9073 (tp) REVERT: D 85 MET cc_start: 0.8723 (mtp) cc_final: 0.8512 (mtm) REVERT: H 78 GLU cc_start: 0.9429 (tt0) cc_final: 0.9155 (tm-30) REVERT: J 58 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8861 (mp10) REVERT: J 80 ASN cc_start: 0.9041 (t0) cc_final: 0.8286 (p0) REVERT: N 97 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: N 255 ASP cc_start: 0.9499 (m-30) cc_final: 0.9152 (m-30) REVERT: E 55 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8265 (p0) REVERT: R 29 LYS cc_start: 0.9329 (mttt) cc_final: 0.9090 (mmtt) REVERT: Q 113 ASP cc_start: 0.9382 (m-30) cc_final: 0.8831 (t0) REVERT: M 309 ASP cc_start: 0.9269 (m-30) cc_final: 0.8965 (p0) REVERT: S 78 GLU cc_start: 0.9374 (tt0) cc_final: 0.9083 (tp30) outliers start: 46 outliers final: 26 residues processed: 274 average time/residue: 0.4586 time to fit residues: 205.0950 Evaluate side-chains 271 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 281 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 339 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN L 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33354 Z= 0.297 Angle : 0.561 16.521 45334 Z= 0.260 Chirality : 0.041 0.144 4959 Planarity : 0.004 0.044 5698 Dihedral : 12.076 147.958 5275 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.53 % Allowed : 10.98 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.72 (0.14), residues: 3953 helix: 1.75 (0.11), residues: 2114 sheet: 0.79 (0.27), residues: 365 loop : 0.49 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.011 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.032 0.002 TYR Q 119 ARG 0.004 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9009 (ttp) cc_final: 0.8314 (mmt) REVERT: C 282 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8953 (tp) REVERT: P 62 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8771 (mtm110) REVERT: P 130 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.7150 (ttp-170) REVERT: P 158 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8004 (ttmm) REVERT: P 196 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7729 (tp) REVERT: G 112 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.9068 (tm-30) REVERT: A 390 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8907 (mtmm) REVERT: B 168 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: B 373 ILE cc_start: 0.9336 (mm) cc_final: 0.9095 (tp) REVERT: H 78 GLU cc_start: 0.9440 (tt0) cc_final: 0.9161 (tm-30) REVERT: J 58 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8873 (mp10) REVERT: J 74 GLU cc_start: 0.9063 (tt0) cc_final: 0.8832 (tm-30) REVERT: J 80 ASN cc_start: 0.9046 (t0) cc_final: 0.8310 (p0) REVERT: N 97 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: N 255 ASP cc_start: 0.9498 (m-30) cc_final: 0.9145 (m-30) REVERT: E 55 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8210 (p0) REVERT: R 29 LYS cc_start: 0.9314 (mttt) cc_final: 0.9079 (mmtt) REVERT: Q 113 ASP cc_start: 0.9374 (m-30) cc_final: 0.8833 (t0) REVERT: M 292 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9029 (p) REVERT: M 309 ASP cc_start: 0.9273 (m-30) cc_final: 0.8949 (p0) REVERT: S 78 GLU cc_start: 0.9382 (tt0) cc_final: 0.9078 (tp30) outliers start: 51 outliers final: 30 residues processed: 276 average time/residue: 0.4518 time to fit residues: 204.0059 Evaluate side-chains 275 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 353 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 6.9990 chunk 340 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 175 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 157 GLN A 192 GLN D 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33354 Z= 0.232 Angle : 0.518 16.101 45334 Z= 0.244 Chirality : 0.040 0.141 4959 Planarity : 0.004 0.045 5698 Dihedral : 11.745 148.468 5270 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.26 % Allowed : 11.40 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.84 (0.14), residues: 3953 helix: 1.84 (0.11), residues: 2119 sheet: 0.84 (0.28), residues: 365 loop : 0.53 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.024 0.001 TYR Q 119 ARG 0.003 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 240 time to evaluate : 4.075 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.9000 (ttp) cc_final: 0.8304 (mmt) REVERT: P 130 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.7044 (ttp-170) REVERT: P 158 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8019 (ttmm) REVERT: G 112 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9077 (tm-30) REVERT: B 168 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: B 373 ILE cc_start: 0.9323 (mm) cc_final: 0.9096 (tp) REVERT: H 78 GLU cc_start: 0.9442 (tt0) cc_final: 0.9154 (tm-30) REVERT: J 58 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8863 (mp10) REVERT: J 74 GLU cc_start: 0.9062 (tt0) cc_final: 0.8831 (tm-30) REVERT: J 80 ASN cc_start: 0.9035 (t0) cc_final: 0.8312 (p0) REVERT: N 255 ASP cc_start: 0.9509 (m-30) cc_final: 0.9167 (m-30) REVERT: E 55 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8143 (p0) REVERT: R 29 LYS cc_start: 0.9319 (mttt) cc_final: 0.9079 (mmtt) REVERT: Q 113 ASP cc_start: 0.9375 (m-30) cc_final: 0.8841 (t0) REVERT: M 292 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9048 (p) REVERT: M 309 ASP cc_start: 0.9278 (m-30) cc_final: 0.8937 (p0) REVERT: S 78 GLU cc_start: 0.9368 (tt0) cc_final: 0.9087 (tp30) REVERT: U 10 LYS cc_start: 0.9060 (tppt) cc_final: 0.8745 (ttpp) outliers start: 42 outliers final: 24 residues processed: 270 average time/residue: 0.4423 time to fit residues: 197.0933 Evaluate side-chains 263 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 376 optimal weight: 0.6980 chunk 235 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 132 HIS L 323 ASN U 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33354 Z= 0.142 Angle : 0.478 16.208 45334 Z= 0.227 Chirality : 0.039 0.141 4959 Planarity : 0.004 0.044 5698 Dihedral : 11.352 148.718 5268 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.05 % Allowed : 11.76 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.96 (0.14), residues: 3953 helix: 1.94 (0.11), residues: 2127 sheet: 0.91 (0.27), residues: 365 loop : 0.57 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 142 HIS 0.005 0.001 HIS C 197 PHE 0.015 0.001 PHE A 334 TYR 0.026 0.001 TYR Q 119 ARG 0.003 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9000 (ttp) cc_final: 0.8302 (mmt) REVERT: P 62 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8684 (mtm110) REVERT: P 162 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8272 (tp) REVERT: P 164 MET cc_start: 0.8895 (mtm) cc_final: 0.8692 (mtm) REVERT: G 112 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9083 (tm-30) REVERT: B 373 ILE cc_start: 0.9325 (mm) cc_final: 0.9102 (tp) REVERT: H 78 GLU cc_start: 0.9413 (tt0) cc_final: 0.9127 (tm-30) REVERT: J 74 GLU cc_start: 0.9054 (tt0) cc_final: 0.8827 (tm-30) REVERT: J 80 ASN cc_start: 0.9025 (t0) cc_final: 0.8296 (p0) REVERT: N 255 ASP cc_start: 0.9499 (m-30) cc_final: 0.9139 (m-30) REVERT: E 55 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8106 (p0) REVERT: R 29 LYS cc_start: 0.9308 (mttt) cc_final: 0.9076 (mmtt) REVERT: Q 113 ASP cc_start: 0.9361 (m-30) cc_final: 0.8850 (t0) REVERT: M 292 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9064 (p) REVERT: M 309 ASP cc_start: 0.9273 (m-30) cc_final: 0.8917 (p0) REVERT: S 78 GLU cc_start: 0.9341 (tt0) cc_final: 0.9088 (tp30) REVERT: U 10 LYS cc_start: 0.9057 (tppt) cc_final: 0.8752 (ttpp) outliers start: 35 outliers final: 23 residues processed: 275 average time/residue: 0.4499 time to fit residues: 204.6414 Evaluate side-chains 264 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33354 Z= 0.234 Angle : 0.511 16.827 45334 Z= 0.242 Chirality : 0.040 0.141 4959 Planarity : 0.004 0.046 5698 Dihedral : 11.325 148.201 5268 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.20 % Allowed : 11.61 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.99 (0.14), residues: 3953 helix: 1.98 (0.11), residues: 2114 sheet: 0.91 (0.27), residues: 365 loop : 0.58 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.023 0.001 TYR Q 119 ARG 0.003 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 3.847 Fit side-chains revert: symmetry clash REVERT: P 62 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8655 (mtm110) REVERT: P 102 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8848 (mmtp) REVERT: P 158 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8074 (ttmm) REVERT: G 112 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9093 (tm-30) REVERT: F 119 TYR cc_start: 0.8561 (t80) cc_final: 0.8308 (t80) REVERT: B 373 ILE cc_start: 0.9322 (mm) cc_final: 0.9096 (tp) REVERT: H 78 GLU cc_start: 0.9407 (tt0) cc_final: 0.9130 (tm-30) REVERT: J 58 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8813 (mp10) REVERT: J 74 GLU cc_start: 0.9036 (tt0) cc_final: 0.8816 (tm-30) REVERT: J 80 ASN cc_start: 0.9032 (t0) cc_final: 0.8312 (p0) REVERT: N 255 ASP cc_start: 0.9498 (m-30) cc_final: 0.9159 (m-30) REVERT: E 55 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8128 (p0) REVERT: R 29 LYS cc_start: 0.9307 (mttt) cc_final: 0.9090 (mmtt) REVERT: Q 113 ASP cc_start: 0.9367 (m-30) cc_final: 0.8856 (t0) REVERT: M 292 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9054 (p) REVERT: M 309 ASP cc_start: 0.9289 (m-30) cc_final: 0.8916 (p0) REVERT: S 78 GLU cc_start: 0.9353 (tt0) cc_final: 0.9100 (tp30) REVERT: U 10 LYS cc_start: 0.9047 (tppt) cc_final: 0.8752 (ttpp) REVERT: U 69 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8833 (pp20) outliers start: 40 outliers final: 30 residues processed: 266 average time/residue: 0.4588 time to fit residues: 198.6286 Evaluate side-chains 271 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 9.9990 chunk 361 optimal weight: 0.0970 chunk 329 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 360 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 317 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33354 Z= 0.131 Angle : 0.470 15.347 45334 Z= 0.224 Chirality : 0.039 0.140 4959 Planarity : 0.004 0.045 5698 Dihedral : 10.965 148.414 5268 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.75 % Allowed : 11.97 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.06 (0.14), residues: 3953 helix: 2.03 (0.11), residues: 2123 sheet: 0.84 (0.27), residues: 367 loop : 0.64 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.004 0.000 HIS B 87 PHE 0.015 0.001 PHE A 334 TYR 0.024 0.001 TYR Q 119 ARG 0.004 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 3.942 Fit side-chains revert: symmetry clash REVERT: P 62 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8610 (mtm110) REVERT: G 112 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9116 (tm-30) REVERT: F 114 TYR cc_start: 0.8086 (t80) cc_final: 0.7877 (t80) REVERT: F 119 TYR cc_start: 0.8485 (t80) cc_final: 0.8231 (t80) REVERT: B 373 ILE cc_start: 0.9322 (mm) cc_final: 0.9110 (tt) REVERT: H 78 GLU cc_start: 0.9390 (tt0) cc_final: 0.9106 (tm-30) REVERT: J 74 GLU cc_start: 0.9038 (tt0) cc_final: 0.8810 (tm-30) REVERT: J 80 ASN cc_start: 0.9022 (t0) cc_final: 0.8293 (p0) REVERT: N 255 ASP cc_start: 0.9482 (m-30) cc_final: 0.9122 (m-30) REVERT: E 55 ASP cc_start: 0.8888 (m-30) cc_final: 0.8108 (p0) REVERT: R 29 LYS cc_start: 0.9299 (mttt) cc_final: 0.9074 (mmtt) REVERT: Q 113 ASP cc_start: 0.9348 (m-30) cc_final: 0.8857 (t0) REVERT: M 292 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9079 (p) REVERT: M 309 ASP cc_start: 0.9278 (m-30) cc_final: 0.8891 (p0) REVERT: S 78 GLU cc_start: 0.9320 (tt0) cc_final: 0.9089 (tp30) REVERT: U 10 LYS cc_start: 0.9049 (tppt) cc_final: 0.8747 (ttpp) REVERT: U 69 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8842 (pp20) outliers start: 25 outliers final: 17 residues processed: 264 average time/residue: 0.4687 time to fit residues: 200.3971 Evaluate side-chains 257 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 9.9990 chunk 230 optimal weight: 0.0370 chunk 371 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 389 optimal weight: 0.0170 chunk 358 optimal weight: 0.0980 chunk 310 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33354 Z= 0.122 Angle : 0.464 14.549 45334 Z= 0.221 Chirality : 0.038 0.139 4959 Planarity : 0.004 0.045 5698 Dihedral : 10.603 148.217 5266 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.69 % Allowed : 12.15 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.13 (0.14), residues: 3953 helix: 2.03 (0.11), residues: 2159 sheet: 0.96 (0.27), residues: 369 loop : 0.71 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.004 0.000 HIS C 197 PHE 0.015 0.001 PHE A 334 TYR 0.027 0.001 TYR Q 119 ARG 0.004 0.000 ARG P 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 3.425 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.9004 (ttp) cc_final: 0.8344 (mmt) REVERT: P 62 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8540 (mtm110) REVERT: P 68 MET cc_start: 0.8639 (mmt) cc_final: 0.8359 (mmt) REVERT: P 164 MET cc_start: 0.8919 (mtm) cc_final: 0.8632 (mpp) REVERT: P 201 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7301 (mmm-85) REVERT: F 114 TYR cc_start: 0.8007 (t80) cc_final: 0.7804 (t80) REVERT: F 119 TYR cc_start: 0.8476 (t80) cc_final: 0.8228 (t80) REVERT: B 373 ILE cc_start: 0.9332 (mm) cc_final: 0.9126 (tt) REVERT: H 78 GLU cc_start: 0.9412 (tt0) cc_final: 0.9131 (tm-30) REVERT: J 74 GLU cc_start: 0.9030 (tt0) cc_final: 0.8800 (tm-30) REVERT: J 80 ASN cc_start: 0.9007 (t0) cc_final: 0.8278 (p0) REVERT: N 255 ASP cc_start: 0.9487 (m-30) cc_final: 0.9099 (m-30) REVERT: E 55 ASP cc_start: 0.8892 (m-30) cc_final: 0.8138 (p0) REVERT: R 29 LYS cc_start: 0.9298 (mttt) cc_final: 0.9079 (mmtt) REVERT: Q 113 ASP cc_start: 0.9327 (m-30) cc_final: 0.8850 (t0) REVERT: S 78 GLU cc_start: 0.9297 (tt0) cc_final: 0.9082 (tp30) REVERT: U 69 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8849 (pp20) outliers start: 23 outliers final: 16 residues processed: 263 average time/residue: 0.4499 time to fit residues: 197.0493 Evaluate side-chains 256 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 0.9980 chunk 246 optimal weight: 0.5980 chunk 330 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 310 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 377 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.047752 restraints weight = 92958.000| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.29 r_work: 0.2610 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33354 Z= 0.138 Angle : 0.473 14.702 45334 Z= 0.223 Chirality : 0.039 0.140 4959 Planarity : 0.004 0.045 5698 Dihedral : 10.491 147.762 5263 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.69 % Allowed : 12.24 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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 (0.14), residues: 3953 helix: 2.08 (0.11), residues: 2154 sheet: 0.98 (0.27), residues: 371 loop : 0.75 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 79 HIS 0.005 0.000 HIS C 197 PHE 0.015 0.001 PHE A 334 TYR 0.022 0.001 TYR Q 119 ARG 0.003 0.000 ARG P 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6663.71 seconds wall clock time: 124 minutes 5.59 seconds (7445.59 seconds total)