Starting phenix.real_space_refine on Sat Dec 16 02:46:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab7_15313/12_2023/8ab7_15313_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 P 30 5.49 5 S 110 5.16 5 Cl 2 4.86 5 C 21754 2.51 5 N 5472 2.21 5 O 6276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" 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 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" 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 "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" 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 "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" 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 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "L TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33654 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: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} 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: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 313 Unusual residues: {'AOQ': 1, 'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'HEC': 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: "H" 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: 111 Unresolved non-hydrogen dihedrals: 111 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: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 363 Unusual residues: {'AOQ': 1, 'AWB': 1, 'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.588 51.844 37.435 1.00 54.19 S ATOM 4207 SG CYS P 187 32.328 49.243 37.027 1.00 36.86 S ATOM 20227 SG CYS E 168 87.591 77.054 37.439 1.00 54.82 S ATOM 20364 SG CYS E 187 84.854 79.657 37.028 1.00 36.40 S Time building chain proxies: 17.71, per 1000 atoms: 0.53 Number of scatterers: 33654 At special positions: 0 Unit cell: (118.017, 128.898, 162.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 10 26.01 Cl 2 17.00 S 110 16.00 P 30 15.00 O 6276 8.00 N 5472 7.00 C 21754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.09 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=2.07 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 189 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.05 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.08 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 170 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 190 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 168 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 187 " 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 : 6 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 18 sheets defined 52.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.47 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: 3.892A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.629A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.547A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 156 through 166 removed outlier: 3.894A pdb=" N GLU C 159 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 203 Proline residue: C 187 - end of helix removed outlier: 4.056A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.698A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.908A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.970A 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: 4.053A 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: 3.575A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.617A 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 136 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.601A 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: 3.523A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.242A 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: 3.783A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.878A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.968A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.520A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 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 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.023A 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: 3.811A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.553A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.395A 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: 3.675A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.971A 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 77 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.583A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.219A 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: 3.521A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.753A 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: 3.569A 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 218 removed outlier: 3.508A 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: 4.339A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.513A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) 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: 4.825A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.509A 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: 3.891A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY N 47 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.622A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.711A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 149 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: 4.053A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.732A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.924A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.967A 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: 4.053A 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: 3.589A 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: 4.888A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 138 Processing helix chain 'E' and resid 152 through 155 No H-bonds generated for 'chain 'E' and resid 152 through 155' 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: 3.586A 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 136 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.600A 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 removed outlier: 3.506A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.783A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.876A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.971A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.116A 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 205 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 Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.021A 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: 3.818A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.584A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.382A 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: 3.683A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.979A 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: 3.675A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.224A 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: 3.522A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.726A pdb=" N LEU M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 334 through 353 Processing helix chain 'M' and resid 355 through 366 removed outlier: 3.858A 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 No H-bonds generated for 'chain 'O' and resid 135 through 138' Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.507A 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: 4.312A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.516A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) 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: 4.826A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.573A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.861A 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 removed outlier: 3.543A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) 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: 4.037A 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: 3.550A 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 'E' and resid 103 through 106 Processing sheet with id= L, first strand: chain 'E' and resid 114 through 120 removed outlier: 3.861A pdb=" N LYS E 114 " --> pdb=" O HIS E 129 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.538A pdb=" N SER E 192 " --> pdb=" O CYS E 187 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= O, first strand: chain 'L' and resid 266 through 271 Processing sheet with id= P, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.044A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 231 through 235 removed outlier: 3.515A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'O' and resid 156 through 158 1597 hydrogen bonds defined for protein. 4350 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: 12.66 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 10690 1.35 - 1.57: 23526 1.57 - 1.78: 90 1.78 - 2.00: 186 2.00 - 2.22: 22 Bond restraints: 34514 Sorted by residual: bond pdb=" C32 CDL A3001 " pdb=" C33 CDL A3001 " ideal model delta sigma weight residual 1.517 1.705 -0.188 1.70e-02 3.46e+03 1.22e+02 bond pdb=" C14 CDL N 504 " pdb=" C15 CDL N 504 " ideal model delta sigma weight residual 1.517 1.764 -0.247 2.70e-02 1.37e+03 8.40e+01 bond pdb=" C34 CDL A3001 " pdb=" C35 CDL A3001 " ideal model delta sigma weight residual 1.517 1.764 -0.247 2.70e-02 1.37e+03 8.35e+01 bond pdb=" C21 AWB N 508 " pdb=" N1 AWB N 508 " ideal model delta sigma weight residual 1.493 1.316 0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" C21 AWB C 507 " pdb=" N1 AWB C 507 " ideal model delta sigma weight residual 1.493 1.322 0.171 2.00e-02 2.50e+03 7.34e+01 ... (remaining 34509 not shown) Histogram of bond angle deviations from ideal: 85.23 - 104.09: 910 104.09 - 122.94: 40908 122.94 - 141.80: 5084 141.80 - 160.65: 0 160.65 - 179.51: 12 Bond angle restraints: 46914 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.52 15.81 1.14e+00 7.69e-01 1.92e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 88.55 15.78 1.14e+00 7.69e-01 1.92e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 89.65 14.68 1.20e+00 6.94e-01 1.50e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 89.71 14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" CG ARG P 62 " pdb=" CD ARG P 62 " pdb=" NE ARG P 62 " ideal model delta sigma weight residual 112.00 137.08 -25.08 2.20e+00 2.07e-01 1.30e+02 ... (remaining 46909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.10: 19239 31.10 - 62.20: 1230 62.20 - 93.30: 134 93.30 - 124.40: 9 124.40 - 155.51: 6 Dihedral angle restraints: 20618 sinusoidal: 8646 harmonic: 11972 Sorted by residual: dihedral pdb=" C HIS Q 96 " pdb=" N HIS Q 96 " pdb=" CA HIS Q 96 " pdb=" CB HIS Q 96 " ideal model delta harmonic sigma weight residual -122.60 -98.06 -24.54 0 2.50e+00 1.60e-01 9.64e+01 dihedral pdb=" C GLU Q 100 " pdb=" N GLU Q 100 " pdb=" CA GLU Q 100 " pdb=" CB GLU Q 100 " ideal model delta harmonic sigma weight residual -122.60 -101.43 -21.17 0 2.50e+00 1.60e-01 7.17e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -102.46 -20.14 0 2.50e+00 1.60e-01 6.49e+01 ... (remaining 20615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 4880 0.232 - 0.465: 230 0.465 - 0.697: 7 0.697 - 0.930: 5 0.930 - 1.162: 2 Chirality restraints: 5124 Sorted by residual: chirality pdb=" C16 AOQ N 509 " pdb=" C11 AOQ N 509 " pdb=" C15 AOQ N 509 " pdb=" C2 AOQ N 509 " both_signs ideal model delta sigma weight residual False 2.79 1.63 1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" C16 AOQ C 508 " pdb=" C11 AOQ C 508 " pdb=" C15 AOQ C 508 " pdb=" C2 AOQ C 508 " both_signs ideal model delta sigma weight residual False 2.79 1.71 1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.68 -0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 5121 not shown) Planarity restraints: 5896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 508 " -0.132 2.00e-02 2.50e+03 1.49e-01 2.21e+02 pdb=" C21 AWB N 508 " 0.173 2.00e-02 2.50e+03 pdb=" N1 AWB N 508 " 0.121 2.00e-02 2.50e+03 pdb=" O5 AWB N 508 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 507 " 0.127 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" C21 AWB C 507 " -0.154 2.00e-02 2.50e+03 pdb=" N1 AWB C 507 " -0.124 2.00e-02 2.50e+03 pdb=" O5 AWB C 507 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 96 " -0.090 2.00e-02 2.50e+03 7.57e-02 8.60e+01 pdb=" CG HIS F 96 " 0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS F 96 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 HIS F 96 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 HIS F 96 " -0.055 2.00e-02 2.50e+03 pdb=" NE2 HIS F 96 " -0.075 2.00e-02 2.50e+03 ... (remaining 5893 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 63 2.48 - 3.08: 23808 3.08 - 3.69: 54867 3.69 - 4.29: 88424 4.29 - 4.90: 136273 Nonbonded interactions: 303435 Sorted by model distance: nonbonded pdb=" OG SER N 152 " pdb=" NZ LYS N 288 " model vdw 1.874 2.520 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.060 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.112 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.164 2.520 ... (remaining 303430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 503)) 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 'E' selection = (chain 'P' and (resid 39 through 224 or resid 301)) } 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' } 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: 2.170 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: 11.780 Check model and map are aligned: 0.430 Set scattering table: 0.310 Process input model: 97.880 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.430 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.013 0.247 34514 Z= 0.826 Angle : 2.004 25.081 46914 Z= 1.257 Chirality : 0.120 1.162 5124 Planarity : 0.008 0.149 5896 Dihedral : 19.385 155.505 12888 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 5.54 % Allowed : 8.60 % Favored : 85.86 % Cbeta Deviations : 2.02 % Peptide Plane: Cis-proline : 2.73 % 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: -1.88 (0.11), residues: 4080 helix: -1.49 (0.09), residues: 2134 sheet: -0.24 (0.24), residues: 358 loop : -0.86 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.009 TRP N 142 HIS 0.056 0.005 HIS F 96 PHE 0.100 0.008 PHE N 129 TYR 0.057 0.008 TYR G 101 ARG 0.029 0.002 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 900 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 30 residues processed: 1014 average time/residue: 0.5065 time to fit residues: 811.6658 Evaluate side-chains 514 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 484 time to evaluate : 3.770 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.3655 time to fit residues: 24.5356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 30.0000 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 366 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 173 ASN C 177 GLN C 253 HIS C 332 ASN P 115 ASN G 84 HIS F 135 ASN A 70 ASN A 74 HIS A 102 HIS A 177 ASN A 192 GLN A 196 ASN A 222 HIS A 371 ASN A 433 HIS B 28 GLN B 87 HIS B 92 HIS D 118 GLN D 208 HIS D 269 GLN D 326 ASN I 49 GLN N 14 ASN N 202 HIS ** N 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN R 84 HIS Q 135 ASN L 70 ASN L 102 HIS L 177 ASN L 192 GLN L 196 ASN L 323 ASN L 371 ASN L 433 HIS ** M 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS M 354 ASN O 118 GLN O 208 HIS O 269 GLN O 326 ASN T 49 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34514 Z= 0.228 Angle : 0.666 16.553 46914 Z= 0.322 Chirality : 0.044 0.286 5124 Planarity : 0.005 0.089 5896 Dihedral : 14.934 148.761 5446 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Rotamer: Outliers : 2.30 % Allowed : 12.92 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.06 (0.13), residues: 4080 helix: 0.26 (0.10), residues: 2156 sheet: 0.39 (0.27), residues: 344 loop : -0.12 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 142 HIS 0.013 0.001 HIS P 190 PHE 0.025 0.002 PHE M 62 TYR 0.019 0.002 TYR N 16 ARG 0.009 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 604 time to evaluate : 3.925 Fit side-chains outliers start: 79 outliers final: 43 residues processed: 659 average time/residue: 0.4819 time to fit residues: 509.6836 Evaluate side-chains 493 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 450 time to evaluate : 3.837 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3364 time to fit residues: 31.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 305 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 397 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN F 97 HIS F 132 HIS A 410 GLN B 197 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN N 177 GLN N 202 HIS ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 332 ASN E 57 ASN E 115 ASN Q 97 HIS Q 132 HIS L 410 GLN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 HIS M 316 GLN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34514 Z= 0.331 Angle : 0.657 16.068 46914 Z= 0.313 Chirality : 0.045 0.272 5124 Planarity : 0.005 0.075 5896 Dihedral : 14.111 141.023 5446 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 1.78 % Allowed : 14.52 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.48 (0.13), residues: 4080 helix: 0.63 (0.11), residues: 2132 sheet: 0.28 (0.25), residues: 376 loop : 0.10 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 142 HIS 0.014 0.002 HIS Q 97 PHE 0.019 0.002 PHE C 90 TYR 0.019 0.002 TYR N 16 ARG 0.004 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 455 time to evaluate : 4.179 Fit side-chains outliers start: 61 outliers final: 45 residues processed: 495 average time/residue: 0.4769 time to fit residues: 384.9448 Evaluate side-chains 457 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 412 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3921 time to fit residues: 36.6599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 349 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 HIS C 202 HIS ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN F 97 HIS B 197 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN I 49 GLN ** N 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN T 49 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34514 Z= 0.330 Angle : 0.645 20.539 46914 Z= 0.302 Chirality : 0.045 0.262 5124 Planarity : 0.005 0.066 5896 Dihedral : 13.674 137.109 5446 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 1.78 % Allowed : 15.69 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.56 (0.13), residues: 4080 helix: 0.76 (0.11), residues: 2110 sheet: 0.07 (0.25), residues: 374 loop : 0.12 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 142 HIS 0.011 0.002 HIS F 92 PHE 0.020 0.002 PHE B 62 TYR 0.020 0.002 TYR E 66 ARG 0.005 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 458 time to evaluate : 3.890 Fit side-chains outliers start: 61 outliers final: 33 residues processed: 509 average time/residue: 0.4575 time to fit residues: 384.4123 Evaluate side-chains 447 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 414 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3483 time to fit residues: 26.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 GLN P 115 ASN B 316 GLN B 354 ASN D 166 ASN N 11 ASN N 253 HIS E 85 GLN E 115 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34514 Z= 0.169 Angle : 0.523 11.680 46914 Z= 0.252 Chirality : 0.041 0.222 5124 Planarity : 0.004 0.048 5896 Dihedral : 13.045 142.758 5446 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 1.14 % Allowed : 17.11 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 0.93 (0.13), residues: 4080 helix: 1.14 (0.11), residues: 2120 sheet: 0.18 (0.26), residues: 356 loop : 0.18 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.005 0.001 HIS E 190 PHE 0.029 0.001 PHE B 62 TYR 0.017 0.001 TYR M 47 ARG 0.007 0.000 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 479 time to evaluate : 3.823 Fit side-chains outliers start: 39 outliers final: 15 residues processed: 504 average time/residue: 0.4634 time to fit residues: 381.8878 Evaluate side-chains 442 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 427 time to evaluate : 4.143 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3240 time to fit residues: 14.5954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 8.9990 chunk 351 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 390 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN B 241 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN E 115 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 ASN M 377 ASN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34514 Z= 0.182 Angle : 0.524 13.061 46914 Z= 0.250 Chirality : 0.041 0.196 5124 Planarity : 0.004 0.044 5896 Dihedral : 12.715 144.595 5446 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.12 (0.13), residues: 4080 helix: 1.31 (0.11), residues: 2114 sheet: 0.10 (0.25), residues: 384 loop : 0.30 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 142 HIS 0.006 0.001 HIS C 197 PHE 0.016 0.001 PHE L 334 TYR 0.018 0.001 TYR M 47 ARG 0.007 0.000 ARG T 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 438 time to evaluate : 3.745 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 454 average time/residue: 0.4580 time to fit residues: 341.7723 Evaluate side-chains 426 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 415 time to evaluate : 4.075 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3232 time to fit residues: 12.0825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN B 64 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN N 73 ASN E 115 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34514 Z= 0.246 Angle : 0.556 14.148 46914 Z= 0.263 Chirality : 0.042 0.194 5124 Planarity : 0.004 0.042 5896 Dihedral : 12.779 143.632 5446 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 0.87 % Allowed : 18.72 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.05 (0.13), residues: 4080 helix: 1.25 (0.11), residues: 2126 sheet: 0.14 (0.26), residues: 362 loop : 0.25 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 PHE 0.017 0.001 PHE B 60 TYR 0.022 0.001 TYR E 66 ARG 0.007 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 426 time to evaluate : 3.865 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 444 average time/residue: 0.4661 time to fit residues: 340.5759 Evaluate side-chains 428 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 406 time to evaluate : 3.795 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3207 time to fit residues: 17.6340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN E 115 ASN M 28 GLN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34514 Z= 0.182 Angle : 0.520 12.835 46914 Z= 0.247 Chirality : 0.041 0.198 5124 Planarity : 0.004 0.043 5896 Dihedral : 12.537 145.370 5446 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 0.70 % Allowed : 18.89 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.21 (0.13), residues: 4080 helix: 1.37 (0.11), residues: 2116 sheet: 0.28 (0.25), residues: 366 loop : 0.32 (0.17), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 142 HIS 0.005 0.001 HIS C 197 PHE 0.019 0.001 PHE N 74 TYR 0.018 0.001 TYR F 114 ARG 0.007 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 429 time to evaluate : 4.067 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 442 average time/residue: 0.4761 time to fit residues: 347.2217 Evaluate side-chains 427 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 413 time to evaluate : 3.902 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3180 time to fit residues: 13.5807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 3.9990 chunk 373 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 chunk 343 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN I 55 HIS N 11 ASN E 115 ASN M 64 ASN M 377 ASN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN T 55 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34514 Z= 0.261 Angle : 0.564 14.768 46914 Z= 0.268 Chirality : 0.043 0.193 5124 Planarity : 0.004 0.044 5896 Dihedral : 12.714 144.402 5446 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 19.18 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.10 (0.13), residues: 4080 helix: 1.26 (0.11), residues: 2124 sheet: 0.18 (0.25), residues: 372 loop : 0.32 (0.17), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.023 0.002 PHE M 60 TYR 0.026 0.002 TYR M 47 ARG 0.007 0.000 ARG T 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 414 time to evaluate : 3.931 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 426 average time/residue: 0.4753 time to fit residues: 334.4155 Evaluate side-chains 410 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 398 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3597 time to fit residues: 13.7060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 383 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 370 optimal weight: 0.8980 chunk 320 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 247 optimal weight: 0.4980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN B 377 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN E 115 ASN M 377 ASN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34514 Z= 0.201 Angle : 0.526 13.302 46914 Z= 0.252 Chirality : 0.041 0.198 5124 Planarity : 0.004 0.045 5896 Dihedral : 12.563 145.426 5446 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 0.12 % Allowed : 19.62 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % 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: 1.18 (0.13), residues: 4080 helix: 1.31 (0.11), residues: 2142 sheet: 0.26 (0.25), residues: 366 loop : 0.34 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 142 HIS 0.006 0.001 HIS M 87 PHE 0.017 0.001 PHE A 334 TYR 0.023 0.001 TYR M 47 ARG 0.007 0.000 ARG A 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 407 time to evaluate : 4.460 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 410 average time/residue: 0.4704 time to fit residues: 319.4784 Evaluate side-chains 398 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 3.884 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3240 time to fit residues: 5.8025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 295 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN E 115 ASN M 377 ASN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.092657 restraints weight = 47709.482| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34514 Z= 0.354 Angle : 0.621 15.501 46914 Z= 0.296 Chirality : 0.045 0.199 5124 Planarity : 0.005 0.054 5896 Dihedral : 12.999 142.585 5446 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 0.38 % Allowed : 19.85 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4080 helix: 1.01 (0.11), residues: 2146 sheet: 0.10 (0.26), residues: 358 loop : 0.27 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 120 HIS 0.009 0.001 HIS C 197 PHE 0.019 0.002 PHE A 334 TYR 0.027 0.002 TYR E 66 ARG 0.011 0.001 ARG I 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8279.69 seconds wall clock time: 151 minutes 20.34 seconds (9080.34 seconds total)