Starting phenix.real_space_refine on Thu Feb 22 01:08:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac3_15332/02_2024/8ac3_15332_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 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 ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" 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 PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 85": "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 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "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 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 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 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 34 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: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 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: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 111 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.060 47.877 30.268 1.00226.78 S ATOM 4207 SG CYS P 187 31.405 45.203 28.735 1.00207.17 S Time building chain proxies: 18.12, per 1000 atoms: 0.56 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 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 6073 8.00 N 5296 7.00 C 21031 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=2.04 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=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.02 Conformation dependent library (CDL) restraints added in 6.2 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 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 15 sheets defined 54.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 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: 3.935A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.755A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.506A pdb=" N ILE C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 4.054A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.298A 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: 4.159A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.829A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.793A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.969A 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: 4.112A 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: 3.636A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 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 61 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: 3.672A 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: 3.600A 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: 3.532A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.844A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.867A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 3.996A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 156 " --> pdb=" O THR A 152 " (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: 3.608A 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: 3.534A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.977A 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: 3.662A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.558A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.382A 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: 3.672A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.969A 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: 3.614A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.218A 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 removed outlier: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.708A 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: 3.722A 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 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 219 removed outlier: 3.564A 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 40 through 81 removed outlier: 4.327A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.749A 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: 5.089A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.511A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.949A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.756A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.505A pdb=" N ILE N 119 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 4.114A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.277A 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: 4.171A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.825A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.797A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.974A 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: 4.108A 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: 3.651A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' 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: 3.688A 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: 3.604A 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: 3.848A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.866A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.998A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.027A 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: 3.533A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.990A 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: 3.665A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.649A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.386A 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: 3.668A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.596A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.206A 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 removed outlier: 3.515A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.712A 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 367 removed outlier: 3.858A 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 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 219 removed outlier: 3.564A 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 40 through 81 removed outlier: 4.332A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.761A 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: 5.096A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.561A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.893A 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: 4.105A 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: 3.599A 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: 4.109A 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: 3.585A 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 1586 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: 10.53 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13594 1.41 - 1.61: 19567 1.61 - 1.82: 169 1.82 - 2.03: 19 2.03 - 2.24: 18 Bond restraints: 33367 Sorted by residual: bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.589 -0.131 1.90e-02 2.77e+03 4.73e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.60e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C2A HEC D 401 " pdb=" C3A HEC D 401 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.00e-02 2.50e+03 3.34e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 83.73 - 102.84: 439 102.84 - 121.94: 38106 121.94 - 141.05: 6795 141.05 - 160.16: 0 160.16 - 179.27: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.21 11.12 1.14e+00 7.69e-01 9.52e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 97.64 13.63 1.47e+00 4.63e-01 8.59e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.32 11.01 1.20e+00 6.94e-01 8.41e+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 99.55 11.72 1.47e+00 4.63e-01 6.35e+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 94.78 17.22 2.20e+00 2.07e-01 6.12e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 18880 32.63 - 65.25: 987 65.25 - 97.88: 92 97.88 - 130.50: 1 130.50 - 163.13: 3 Dihedral angle restraints: 19963 sinusoidal: 8344 harmonic: 11619 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 -105.76 -16.84 0 2.50e+00 1.60e-01 4.54e+01 dihedral pdb=" C ARG H 51 " pdb=" N ARG H 51 " pdb=" CA ARG H 51 " pdb=" CB ARG H 51 " ideal model delta harmonic sigma weight residual -122.60 -138.29 15.69 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.07 63.07 2 1.00e+01 1.00e-02 3.82e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4509 0.190 - 0.379: 426 0.379 - 0.569: 21 0.569 - 0.758: 2 0.758 - 0.948: 4 Chirality restraints: 4962 Sorted by residual: 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 -1.63 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CB4 CDL S 101 " pdb=" CB3 CDL S 101 " pdb=" CB6 CDL S 101 " pdb=" OB6 CDL S 101 " both_signs ideal model delta sigma weight residual False -2.57 -1.64 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.73 -0.85 2.00e-01 2.50e+01 1.80e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.044 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS N 96 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 502 " -0.023 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" C2A HEM C 502 " 0.027 2.00e-02 2.50e+03 pdb=" C3A HEM C 502 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 502 " -0.031 2.00e-02 2.50e+03 pdb=" CAA HEM C 502 " -0.015 2.00e-02 2.50e+03 pdb=" CHA HEM C 502 " 0.036 2.00e-02 2.50e+03 pdb=" CHB HEM C 502 " 0.039 2.00e-02 2.50e+03 pdb=" CMA HEM C 502 " -0.006 2.00e-02 2.50e+03 pdb=" NA HEM C 502 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.014 2.00e-02 2.50e+03 2.73e-02 1.68e+01 pdb=" C2A HEC D 401 " -0.034 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.036 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.041 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.012 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.045 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.003 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.003 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 222 2.62 - 3.19: 28706 3.19 - 3.76: 53443 3.76 - 4.33: 79239 4.33 - 4.90: 121792 Nonbonded interactions: 283402 Sorted by model distance: nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.054 3.080 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.113 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.114 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.219 3.080 ... (remaining 283397 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' and (resid 26 through 474 or resid 3001 through 3002)) 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)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503)) } 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 or resid 101)) } 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: 2.420 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: 11.700 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 90.780 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9242 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 0.200 33367 Z= 0.680 Angle : 1.741 17.216 45352 Z= 1.085 Chirality : 0.116 0.948 4962 Planarity : 0.007 0.039 5700 Dihedral : 18.285 163.126 12462 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 3.85 % Allowed : 7.43 % Favored : 88.72 % 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: -1.48 (0.12), residues: 3955 helix: -1.14 (0.09), residues: 2109 sheet: 0.03 (0.25), residues: 356 loop : -0.71 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.007 TRP A 474 HIS 0.024 0.004 HIS Q 92 PHE 0.047 0.006 PHE B 107 TYR 0.050 0.007 TYR G 101 ARG 0.036 0.002 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 373 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8885 (tptp) REVERT: C 369 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (mtp) REVERT: C 374 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8957 (mt-10) REVERT: P 116 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (m) REVERT: P 134 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9062 (mm-30) REVERT: P 185 TRP cc_start: 0.8079 (m-90) cc_final: 0.7813 (m-90) REVERT: P 199 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8363 (mtm180) REVERT: P 222 LEU cc_start: 0.9563 (pp) cc_final: 0.9246 (pt) REVERT: G 76 ARG cc_start: 0.9490 (OUTLIER) cc_final: 0.8733 (ttm170) REVERT: G 116 LYS cc_start: 0.8810 (tttm) cc_final: 0.8597 (ttmm) REVERT: G 120 ASP cc_start: 0.9382 (m-30) cc_final: 0.9164 (m-30) REVERT: G 123 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: F 88 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8682 (mm-30) REVERT: F 125 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8861 (tt0) REVERT: A 87 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: A 97 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9101 (tp30) REVERT: A 397 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6816 (mt) REVERT: A 402 TYR cc_start: 0.9151 (m-80) cc_final: 0.8830 (m-80) REVERT: B 170 TYR cc_start: 0.8551 (p90) cc_final: 0.8229 (p90) REVERT: B 345 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9242 (mtpp) REVERT: D 160 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9214 (pt0) REVERT: D 166 ASN cc_start: 0.8959 (m110) cc_final: 0.8439 (m-40) REVERT: D 224 GLU cc_start: 0.9310 (tt0) cc_final: 0.8986 (pp20) REVERT: D 248 MET cc_start: 0.9369 (ttp) cc_final: 0.8881 (ttp) REVERT: H 75 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8827 (tm-30) REVERT: H 88 GLU cc_start: 0.9133 (mp0) cc_final: 0.8851 (mp0) REVERT: I 7 PHE cc_start: 0.9035 (t80) cc_final: 0.8827 (m-80) REVERT: J 10 LYS cc_start: 0.9502 (tttm) cc_final: 0.9248 (tptp) REVERT: J 55 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8932 (tpp80) REVERT: N 250 LYS cc_start: 0.9240 (ttmt) cc_final: 0.9024 (ttmm) REVERT: E 55 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8548 (p0) REVERT: Q 88 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8463 (mm-30) REVERT: Q 122 ASP cc_start: 0.8486 (p0) cc_final: 0.8276 (p0) REVERT: L 397 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7303 (mp) REVERT: M 19 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: S 75 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8766 (tm-30) REVERT: S 78 GLU cc_start: 0.9357 (tt0) cc_final: 0.9028 (pp20) REVERT: U 10 LYS cc_start: 0.9399 (tttm) cc_final: 0.8998 (mppt) outliers start: 128 outliers final: 13 residues processed: 465 average time/residue: 1.7232 time to fit residues: 925.4033 Evaluate side-chains 302 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 0.0010 chunk 101 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 158 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 overall best weight: 1.6150 ------------------------------------------------------------------------------- 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 G 84 HIS F 97 HIS F 132 HIS A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 215 GLN B 316 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS Q 132 HIS L 50 GLN L 177 ASN L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 196 ASN M 215 GLN M 241 ASN M 316 GLN M 377 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33367 Z= 0.226 Angle : 0.631 16.871 45352 Z= 0.309 Chirality : 0.042 0.206 4962 Planarity : 0.004 0.043 5700 Dihedral : 14.113 159.784 5324 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.77 % Allowed : 11.37 % Favored : 86.86 % 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: 0.67 (0.13), residues: 3955 helix: 0.80 (0.11), residues: 2124 sheet: 0.52 (0.26), residues: 365 loop : 0.10 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 156 HIS 0.008 0.001 HIS C 197 PHE 0.021 0.002 PHE A 334 TYR 0.019 0.002 TYR O 237 ARG 0.007 0.001 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 295 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8876 (tptp) REVERT: P 115 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7132 (p0) REVERT: P 150 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7556 (mm110) REVERT: P 222 LEU cc_start: 0.9430 (pp) cc_final: 0.9121 (tp) REVERT: G 120 ASP cc_start: 0.9335 (m-30) cc_final: 0.9105 (m-30) REVERT: G 123 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8652 (tm-30) REVERT: F 100 GLU cc_start: 0.8968 (pt0) cc_final: 0.8747 (mt-10) REVERT: F 125 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8796 (tt0) REVERT: F 138 THR cc_start: 0.9105 (m) cc_final: 0.8900 (m) REVERT: A 97 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9174 (tp30) REVERT: A 397 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6825 (mt) REVERT: A 402 TYR cc_start: 0.9140 (m-80) cc_final: 0.8822 (m-80) REVERT: D 160 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9106 (pt0) REVERT: D 166 ASN cc_start: 0.8932 (m110) cc_final: 0.8412 (m-40) REVERT: D 224 GLU cc_start: 0.9381 (tt0) cc_final: 0.9071 (pp20) REVERT: H 51 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.7170 (ptm160) REVERT: H 75 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8849 (tm-30) REVERT: J 13 SER cc_start: 0.9147 (t) cc_final: 0.8825 (p) REVERT: J 55 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8855 (tpp80) REVERT: Q 107 LYS cc_start: 0.9527 (ttmm) cc_final: 0.9052 (tppt) REVERT: Q 110 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8924 (mt-10) REVERT: Q 122 ASP cc_start: 0.8554 (p0) cc_final: 0.8346 (p0) REVERT: M 19 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8723 (tm-30) REVERT: M 60 PHE cc_start: 0.9657 (OUTLIER) cc_final: 0.9128 (t80) REVERT: S 75 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8921 (tm-30) REVERT: S 78 GLU cc_start: 0.9352 (tt0) cc_final: 0.9009 (tm-30) REVERT: S 91 LYS cc_start: 0.9540 (mtpp) cc_final: 0.9330 (mppt) REVERT: U 10 LYS cc_start: 0.9425 (tttm) cc_final: 0.9028 (mppt) outliers start: 59 outliers final: 16 residues processed: 335 average time/residue: 1.6663 time to fit residues: 649.6749 Evaluate side-chains 292 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 269 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 356 optimal weight: 0.0570 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 286 optimal weight: 0.0970 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 85 GLN F 97 HIS A 364 HIS E 85 GLN M 92 HIS M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33367 Z= 0.150 Angle : 0.521 11.464 45352 Z= 0.255 Chirality : 0.040 0.187 4962 Planarity : 0.004 0.051 5700 Dihedral : 12.736 153.279 5286 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.29 % Allowed : 12.54 % Favored : 86.17 % 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: 1.29 (0.14), residues: 3955 helix: 1.35 (0.11), residues: 2147 sheet: 0.80 (0.27), residues: 365 loop : 0.27 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 142 HIS 0.004 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.017 0.001 TYR F 114 ARG 0.004 0.000 ARG P 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 298 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8868 (tptp) REVERT: P 222 LEU cc_start: 0.9430 (pp) cc_final: 0.9143 (tp) REVERT: G 50 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8617 (pt0) REVERT: G 120 ASP cc_start: 0.9337 (m-30) cc_final: 0.9057 (m-30) REVERT: F 100 GLU cc_start: 0.9045 (pt0) cc_final: 0.8628 (mt-10) REVERT: F 125 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8719 (tt0) REVERT: A 97 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9184 (tp30) REVERT: A 402 TYR cc_start: 0.9129 (m-80) cc_final: 0.8827 (m-80) REVERT: B 168 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8917 (mt0) REVERT: D 160 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9087 (pt0) REVERT: D 224 GLU cc_start: 0.9397 (tt0) cc_final: 0.9106 (pp20) REVERT: H 57 LEU cc_start: 0.9093 (tp) cc_final: 0.8876 (tp) REVERT: H 75 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8847 (tm-30) REVERT: J 11 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8726 (tptp) REVERT: J 13 SER cc_start: 0.9169 (t) cc_final: 0.8878 (p) REVERT: J 15 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8671 (ptmm) REVERT: J 55 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8878 (tpp80) REVERT: E 55 ASP cc_start: 0.9030 (p0) cc_final: 0.8741 (p0) REVERT: Q 107 LYS cc_start: 0.9538 (ttmm) cc_final: 0.9168 (tppt) REVERT: Q 110 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8960 (mp0) REVERT: M 19 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8719 (mm-30) REVERT: M 60 PHE cc_start: 0.9615 (OUTLIER) cc_final: 0.8990 (t80) REVERT: O 163 ASP cc_start: 0.9409 (m-30) cc_final: 0.8857 (p0) REVERT: S 75 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8937 (tm-30) REVERT: S 78 GLU cc_start: 0.9346 (tt0) cc_final: 0.8985 (tm-30) REVERT: U 10 LYS cc_start: 0.9386 (tttm) cc_final: 0.9036 (mppt) outliers start: 43 outliers final: 9 residues processed: 329 average time/residue: 1.6368 time to fit residues: 630.7784 Evaluate side-chains 279 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 265 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 357 optimal weight: 0.0770 chunk 378 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 HIS F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33367 Z= 0.295 Angle : 0.571 15.635 45352 Z= 0.270 Chirality : 0.042 0.156 4962 Planarity : 0.004 0.053 5700 Dihedral : 12.214 151.208 5273 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.41 % Allowed : 13.50 % Favored : 85.08 % 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: 1.54 (0.14), residues: 3955 helix: 1.54 (0.11), residues: 2140 sheet: 0.93 (0.27), residues: 365 loop : 0.42 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.013 0.001 HIS C 197 PHE 0.019 0.001 PHE A 334 TYR 0.021 0.001 TYR Q 114 ARG 0.007 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 268 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8846 (tptp) REVERT: P 222 LEU cc_start: 0.9398 (pp) cc_final: 0.9125 (tp) REVERT: G 120 ASP cc_start: 0.9359 (m-30) cc_final: 0.9136 (m-30) REVERT: G 123 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 125 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8736 (tt0) REVERT: A 97 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9233 (tp30) REVERT: A 402 TYR cc_start: 0.9129 (m-80) cc_final: 0.8803 (m-80) REVERT: D 160 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9047 (pt0) REVERT: D 224 GLU cc_start: 0.9404 (tt0) cc_final: 0.9129 (pp20) REVERT: H 75 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8857 (tm-30) REVERT: J 11 LYS cc_start: 0.8905 (tmtt) cc_final: 0.8669 (tptp) REVERT: J 13 SER cc_start: 0.9239 (t) cc_final: 0.9018 (p) REVERT: J 15 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8672 (ptmt) REVERT: J 55 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8866 (tpp80) REVERT: E 55 ASP cc_start: 0.9115 (p0) cc_final: 0.8837 (p0) REVERT: R 112 GLU cc_start: 0.9273 (tm-30) cc_final: 0.9062 (tp30) REVERT: Q 107 LYS cc_start: 0.9529 (ttmm) cc_final: 0.9171 (tppt) REVERT: Q 110 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8935 (mp0) REVERT: Q 112 GLU cc_start: 0.8699 (tp30) cc_final: 0.8488 (tp30) REVERT: M 19 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8716 (mm-30) REVERT: O 163 ASP cc_start: 0.9431 (m-30) cc_final: 0.8883 (p0) REVERT: S 75 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8896 (tm-30) REVERT: S 78 GLU cc_start: 0.9356 (tt0) cc_final: 0.8999 (tm-30) REVERT: U 10 LYS cc_start: 0.9346 (tttm) cc_final: 0.8985 (mppt) outliers start: 47 outliers final: 21 residues processed: 303 average time/residue: 1.6370 time to fit residues: 579.7078 Evaluate side-chains 282 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 259 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 124 VAL Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 215 GLN Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN N 177 GLN Q 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33367 Z= 0.295 Angle : 0.559 14.975 45352 Z= 0.266 Chirality : 0.041 0.181 4962 Planarity : 0.004 0.053 5700 Dihedral : 11.942 151.022 5273 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 13.68 % Favored : 84.75 % 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: 1.64 (0.14), residues: 3955 helix: 1.61 (0.11), residues: 2138 sheet: 0.95 (0.27), residues: 365 loop : 0.49 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.010 0.001 HIS C 197 PHE 0.020 0.001 PHE A 334 TYR 0.023 0.001 TYR Q 114 ARG 0.006 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8865 (tptp) REVERT: P 222 LEU cc_start: 0.9389 (pp) cc_final: 0.9121 (tp) REVERT: G 120 ASP cc_start: 0.9359 (m-30) cc_final: 0.9140 (m-30) REVERT: G 123 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 97 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9125 (tp30) REVERT: A 402 TYR cc_start: 0.9129 (m-80) cc_final: 0.8803 (m-80) REVERT: A 461 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8401 (p0) REVERT: D 160 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9033 (pt0) REVERT: D 224 GLU cc_start: 0.9400 (tt0) cc_final: 0.9122 (pp20) REVERT: H 75 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8871 (tm-30) REVERT: J 13 SER cc_start: 0.9290 (t) cc_final: 0.9077 (p) REVERT: J 15 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8700 (ptmt) REVERT: J 55 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8883 (tpp80) REVERT: E 55 ASP cc_start: 0.9206 (p0) cc_final: 0.8929 (p0) REVERT: R 112 GLU cc_start: 0.9279 (tm-30) cc_final: 0.9064 (tp30) REVERT: Q 107 LYS cc_start: 0.9529 (ttmm) cc_final: 0.9162 (tppt) REVERT: Q 110 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8913 (mp0) REVERT: Q 112 GLU cc_start: 0.8732 (tp30) cc_final: 0.8513 (tp30) REVERT: M 19 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8727 (mm-30) REVERT: O 163 ASP cc_start: 0.9431 (m-30) cc_final: 0.8902 (p0) REVERT: S 75 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8907 (tm-30) REVERT: S 78 GLU cc_start: 0.9358 (tt0) cc_final: 0.9001 (tm-30) REVERT: S 91 LYS cc_start: 0.9561 (mtpp) cc_final: 0.9334 (mppt) REVERT: U 10 LYS cc_start: 0.9338 (tttm) cc_final: 0.8986 (mppt) outliers start: 52 outliers final: 19 residues processed: 307 average time/residue: 1.6536 time to fit residues: 591.5050 Evaluate side-chains 277 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 379 optimal weight: 0.7980 chunk 314 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 199 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN Q 109 GLN Q 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33367 Z= 0.150 Angle : 0.501 11.943 45352 Z= 0.241 Chirality : 0.039 0.146 4962 Planarity : 0.004 0.052 5700 Dihedral : 11.502 149.761 5271 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.11 % Allowed : 14.05 % Favored : 84.84 % 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: 1.82 (0.14), residues: 3955 helix: 1.78 (0.11), residues: 2135 sheet: 1.00 (0.27), residues: 365 loop : 0.56 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 142 HIS 0.004 0.001 HIS B 87 PHE 0.017 0.001 PHE P 126 TYR 0.026 0.001 TYR Q 114 ARG 0.008 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8835 (tptp) REVERT: G 120 ASP cc_start: 0.9347 (m-30) cc_final: 0.9084 (m-30) REVERT: G 123 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 97 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9175 (tp30) REVERT: A 402 TYR cc_start: 0.9124 (m-80) cc_final: 0.8807 (m-80) REVERT: A 461 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8157 (p0) REVERT: D 224 GLU cc_start: 0.9393 (tt0) cc_final: 0.9110 (pp20) REVERT: H 75 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8859 (tm-30) REVERT: J 13 SER cc_start: 0.9305 (t) cc_final: 0.9076 (p) REVERT: J 15 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8756 (ptmt) REVERT: J 55 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8857 (tpp80) REVERT: E 55 ASP cc_start: 0.9180 (p0) cc_final: 0.8899 (p0) REVERT: Q 107 LYS cc_start: 0.9535 (ttmm) cc_final: 0.9186 (tppt) REVERT: Q 110 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8938 (mp0) REVERT: Q 112 GLU cc_start: 0.8757 (tp30) cc_final: 0.8548 (tp30) REVERT: L 87 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7866 (mtt90) REVERT: M 19 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8733 (mm-30) REVERT: M 215 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: M 364 MET cc_start: 0.9292 (mmm) cc_final: 0.9039 (mmm) REVERT: O 163 ASP cc_start: 0.9419 (m-30) cc_final: 0.8873 (p0) REVERT: S 75 GLU cc_start: 0.9223 (mt-10) cc_final: 0.9021 (tm-30) REVERT: S 78 GLU cc_start: 0.9328 (tt0) cc_final: 0.8996 (tm-30) REVERT: S 91 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9327 (mppt) REVERT: U 10 LYS cc_start: 0.9302 (tttm) cc_final: 0.8982 (mppt) outliers start: 37 outliers final: 16 residues processed: 306 average time/residue: 1.6601 time to fit residues: 593.1092 Evaluate side-chains 278 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 215 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 377 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN F 135 ASN N 22 GLN M 377 ASN O 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 33367 Z= 0.153 Angle : 0.495 12.569 45352 Z= 0.238 Chirality : 0.039 0.142 4962 Planarity : 0.004 0.052 5700 Dihedral : 11.175 149.455 5271 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.17 % Allowed : 14.23 % Favored : 84.60 % 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: 3955 helix: 1.86 (0.11), residues: 2142 sheet: 1.07 (0.27), residues: 365 loop : 0.66 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 PHE 0.016 0.001 PHE A 334 TYR 0.027 0.001 TYR Q 114 ARG 0.006 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 271 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8836 (tptp) REVERT: P 130 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7789 (ptm-80) REVERT: G 120 ASP cc_start: 0.9345 (m-30) cc_final: 0.9122 (m-30) REVERT: G 123 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 97 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9127 (tp30) REVERT: A 402 TYR cc_start: 0.9131 (m-80) cc_final: 0.8825 (m-80) REVERT: D 224 GLU cc_start: 0.9404 (tt0) cc_final: 0.9142 (pp20) REVERT: H 75 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8860 (tm-30) REVERT: I 30 ASP cc_start: 0.9145 (t70) cc_final: 0.8892 (t0) REVERT: J 11 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8540 (tptp) REVERT: J 55 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8872 (tpp80) REVERT: N 309 ASP cc_start: 0.9148 (t0) cc_final: 0.8867 (t0) REVERT: E 55 ASP cc_start: 0.9201 (p0) cc_final: 0.8924 (p0) REVERT: Q 107 LYS cc_start: 0.9532 (ttmm) cc_final: 0.9189 (tppt) REVERT: Q 110 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8988 (mp0) REVERT: L 87 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7842 (mtt90) REVERT: M 19 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: M 364 MET cc_start: 0.9281 (mmm) cc_final: 0.9010 (mmm) REVERT: O 163 ASP cc_start: 0.9413 (m-30) cc_final: 0.8877 (p0) REVERT: S 75 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9024 (tm-30) REVERT: S 78 GLU cc_start: 0.9331 (tt0) cc_final: 0.9004 (tm-30) REVERT: U 10 LYS cc_start: 0.9295 (tttm) cc_final: 0.8995 (mppt) outliers start: 39 outliers final: 19 residues processed: 300 average time/residue: 1.6713 time to fit residues: 584.4712 Evaluate side-chains 283 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN M 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33367 Z= 0.180 Angle : 0.511 12.848 45352 Z= 0.244 Chirality : 0.039 0.145 4962 Planarity : 0.004 0.052 5700 Dihedral : 11.012 149.410 5271 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.05 % Allowed : 14.92 % Favored : 84.03 % 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: 1.98 (0.14), residues: 3955 helix: 1.87 (0.11), residues: 2145 sheet: 1.09 (0.27), residues: 365 loop : 0.67 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 PHE 0.023 0.001 PHE P 126 TYR 0.027 0.001 TYR Q 114 ARG 0.010 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 265 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8848 (tptp) REVERT: P 130 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7774 (ptm-80) REVERT: G 120 ASP cc_start: 0.9348 (m-30) cc_final: 0.9127 (m-30) REVERT: G 123 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 97 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9130 (tp30) REVERT: A 402 TYR cc_start: 0.9127 (m-80) cc_final: 0.8817 (m-80) REVERT: D 224 GLU cc_start: 0.9408 (tt0) cc_final: 0.9147 (pp20) REVERT: H 75 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8864 (tm-30) REVERT: I 30 ASP cc_start: 0.9155 (t70) cc_final: 0.8877 (t0) REVERT: J 11 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8510 (tptp) REVERT: J 15 LYS cc_start: 0.9217 (ptmt) cc_final: 0.9012 (pttt) REVERT: J 55 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8865 (tpp80) REVERT: N 309 ASP cc_start: 0.9145 (t0) cc_final: 0.8871 (t0) REVERT: E 55 ASP cc_start: 0.9229 (p0) cc_final: 0.8946 (p0) REVERT: Q 107 LYS cc_start: 0.9526 (ttmm) cc_final: 0.9181 (tppt) REVERT: Q 110 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8964 (mp0) REVERT: L 87 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7809 (mtt90) REVERT: M 364 MET cc_start: 0.9268 (mmm) cc_final: 0.8972 (mmm) REVERT: O 163 ASP cc_start: 0.9411 (m-30) cc_final: 0.8886 (p0) REVERT: S 78 GLU cc_start: 0.9338 (tt0) cc_final: 0.9011 (tm-30) REVERT: S 91 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9316 (mppt) REVERT: U 10 LYS cc_start: 0.9281 (tttm) cc_final: 0.8972 (mppt) outliers start: 35 outliers final: 20 residues processed: 289 average time/residue: 1.7189 time to fit residues: 577.3555 Evaluate side-chains 279 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 352 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS M 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33367 Z= 0.179 Angle : 0.511 12.400 45352 Z= 0.244 Chirality : 0.039 0.144 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.864 149.256 5268 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.90 % Allowed : 15.10 % Favored : 84.00 % 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: 2.01 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2145 sheet: 1.08 (0.27), residues: 365 loop : 0.69 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.027 0.001 TYR Q 114 ARG 0.006 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 265 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8845 (tptp) REVERT: P 130 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7769 (ptm-80) REVERT: G 120 ASP cc_start: 0.9347 (m-30) cc_final: 0.9128 (m-30) REVERT: G 123 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 97 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9131 (tp30) REVERT: A 402 TYR cc_start: 0.9125 (m-80) cc_final: 0.8816 (m-80) REVERT: D 224 GLU cc_start: 0.9391 (tt0) cc_final: 0.9137 (pp20) REVERT: H 75 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8855 (tm-30) REVERT: I 30 ASP cc_start: 0.9093 (t70) cc_final: 0.8815 (t0) REVERT: J 11 LYS cc_start: 0.8745 (tmtt) cc_final: 0.8488 (tptp) REVERT: J 15 LYS cc_start: 0.9230 (ptmt) cc_final: 0.8989 (pttm) REVERT: J 55 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8867 (tpp80) REVERT: N 309 ASP cc_start: 0.9141 (t0) cc_final: 0.8865 (t0) REVERT: E 55 ASP cc_start: 0.9237 (p0) cc_final: 0.8960 (p0) REVERT: Q 107 LYS cc_start: 0.9526 (ttmm) cc_final: 0.9179 (tppt) REVERT: Q 110 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8957 (mp0) REVERT: Q 120 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (mmtm) REVERT: L 87 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7819 (mtt90) REVERT: M 364 MET cc_start: 0.9258 (mmm) cc_final: 0.8950 (mmm) REVERT: O 163 ASP cc_start: 0.9405 (m-30) cc_final: 0.8884 (p0) REVERT: S 78 GLU cc_start: 0.9331 (tt0) cc_final: 0.9012 (tm-30) REVERT: S 91 LYS cc_start: 0.9543 (mtpp) cc_final: 0.9309 (mppt) REVERT: U 10 LYS cc_start: 0.9268 (tttm) cc_final: 0.8968 (mppt) outliers start: 30 outliers final: 22 residues processed: 286 average time/residue: 1.6441 time to fit residues: 549.1266 Evaluate side-chains 283 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain N residue 130 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 227 optimal weight: 0.2980 chunk 176 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 390 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 109 GLN M 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33367 Z= 0.242 Angle : 0.545 13.591 45352 Z= 0.259 Chirality : 0.040 0.147 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.912 149.506 5268 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.99 % Allowed : 15.07 % Favored : 83.94 % 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: 1.98 (0.14), residues: 3955 helix: 1.85 (0.11), residues: 2147 sheet: 1.11 (0.27), residues: 365 loop : 0.70 (0.18), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.010 0.001 HIS C 197 PHE 0.026 0.001 PHE P 126 TYR 0.028 0.001 TYR Q 114 ARG 0.007 0.000 ARG P 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 264 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8854 (tptp) REVERT: P 130 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7720 (ptm-80) REVERT: G 120 ASP cc_start: 0.9361 (m-30) cc_final: 0.9145 (m-30) REVERT: F 100 GLU cc_start: 0.8782 (mp0) cc_final: 0.8462 (mp0) REVERT: A 97 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.9138 (tp30) REVERT: A 402 TYR cc_start: 0.9136 (m-80) cc_final: 0.8822 (m-80) REVERT: D 224 GLU cc_start: 0.9392 (tt0) cc_final: 0.9137 (pp20) REVERT: H 75 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8858 (tm-30) REVERT: I 30 ASP cc_start: 0.9124 (t70) cc_final: 0.8844 (t0) REVERT: J 11 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8482 (tptp) REVERT: J 55 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8879 (tpp80) REVERT: E 55 ASP cc_start: 0.9262 (p0) cc_final: 0.8991 (p0) REVERT: Q 110 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8972 (mp0) REVERT: Q 120 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8534 (mmtm) REVERT: L 87 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7856 (mtt90) REVERT: M 364 MET cc_start: 0.9239 (mmm) cc_final: 0.8923 (mmm) REVERT: O 163 ASP cc_start: 0.9415 (m-30) cc_final: 0.8881 (p0) REVERT: S 78 GLU cc_start: 0.9352 (tt0) cc_final: 0.9032 (tm-30) REVERT: U 10 LYS cc_start: 0.9264 (tttm) cc_final: 0.8967 (mppt) outliers start: 33 outliers final: 20 residues processed: 286 average time/residue: 1.6736 time to fit residues: 558.7671 Evaluate side-chains 284 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain N residue 130 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 120 LYS Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 286 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 311 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.046866 restraints weight = 82782.507| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.24 r_work: 0.2549 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33367 Z= 0.277 Angle : 0.563 13.613 45352 Z= 0.267 Chirality : 0.041 0.146 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.979 149.706 5268 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.87 % Allowed : 15.22 % Favored : 83.91 % 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: 1.97 (0.14), residues: 3955 helix: 1.84 (0.11), residues: 2144 sheet: 1.01 (0.27), residues: 375 loop : 0.72 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.011 0.001 HIS C 197 PHE 0.019 0.001 PHE A 334 TYR 0.030 0.001 TYR Q 114 ARG 0.006 0.000 ARG P 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10453.06 seconds wall clock time: 189 minutes 18.64 seconds (11358.64 seconds total)