Starting phenix.real_space_refine on Tue Feb 13 15:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ll6_4071/02_2024/5ll6_4071_updated.pdb" } resolution = 3.9 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= 0.013 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 8 7.16 5 P 1331 5.49 5 Mg 1 5.21 5 S 72 5.16 5 C 29720 2.51 5 N 10027 2.21 5 O 14103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 41": "NH1" <-> "NH2" Residue "P PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "R PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 200": "NH1" <-> "NH2" Residue "S ARG 252": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "U TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 47": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "V ARG 194": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 17": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 78": "NH1" <-> "NH2" Residue "W ARG 168": "NH1" <-> "NH2" Residue "W ARG 171": "NH1" <-> "NH2" Residue "X ARG 30": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 116": "NH1" <-> "NH2" Residue "Y ARG 104": "NH1" <-> "NH2" Residue "Y ARG 106": "NH1" <-> "NH2" Residue "Y PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 90": "NH1" <-> "NH2" Residue "Z ARG 103": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "b PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 144": "NH1" <-> "NH2" Residue "d ARG 20": "NH1" <-> "NH2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 10": "NH1" <-> "NH2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "h ARG 22": "NH1" <-> "NH2" Residue "h PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 101": "NH1" <-> "NH2" Residue "h GLU 151": "OE1" <-> "OE2" Residue "h TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 162": "OD1" <-> "OD2" Residue "h ARG 194": "NH1" <-> "NH2" Residue "h ASP 218": "OD1" <-> "OD2" Residue "h PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 241": "OD1" <-> "OD2" Residue "h PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 289": "OD1" <-> "OD2" Residue "h ARG 311": "NH1" <-> "NH2" Residue "h ARG 328": "NH1" <-> "NH2" Residue "h PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 487": "OD1" <-> "OD2" Residue "h ASP 492": "OD1" <-> "OD2" Residue "h ASP 499": "OD1" <-> "OD2" Residue "h TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 573": "NH1" <-> "NH2" Residue "h ASP 591": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 55262 Number of models: 1 Model: "" Number of chains: 20 Chain: "2" Number of atoms: 28237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1325, 28237 Classifications: {'RNA': 1325} Modifications used: {'rna2p_pur': 51, 'rna2p_pyr': 42, 'rna3p_pur': 652, 'rna3p_pyr': 580} Link IDs: {'rna2p': 93, 'rna3p': 1231} Chain breaks: 5 Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1577 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "R" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1717 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "S" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 172} Chain: "V" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "W" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "X" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1213 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "Z" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 891 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "a" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1060 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "e" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4657 Unusual residues: {' MG': 1, 'ANP': 2, 'SF4': 2} Classifications: {'peptide': 578, 'undetermined': 5} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 543, None: 5} Not linked: pdbres="ASP h 604 " pdbres="SF4 h 701 " Not linked: pdbres="SF4 h 701 " pdbres="SF4 h 702 " Not linked: pdbres="SF4 h 702 " pdbres="ANP h 703 " Not linked: pdbres="ANP h 703 " pdbres=" MG h 704 " Not linked: pdbres=" MG h 704 " pdbres="ANP h 705 " Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 50808 SG CYS h 29 93.313 94.937 142.717 1.00 35.87 S ATOM 51001 SG CYS h 55 99.342 94.944 146.873 1.00 50.48 S ATOM 51037 SG CYS h 61 97.871 98.555 141.785 1.00 25.67 S ATOM 51019 SG CYS h 58 99.197 93.384 141.760 1.00 31.14 S ATOM 50776 SG CYS h 25 94.684 103.092 141.529 1.00 38.66 S ATOM 50741 SG CYS h 21 90.903 108.408 139.545 1.00 48.90 S ATOM 51068 SG CYS h 65 96.483 105.973 139.307 1.00 47.82 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 21756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 21756 " occ=0.55 Time building chain proxies: 21.47, per 1000 atoms: 0.39 Number of scatterers: 55262 At special positions: 0 Unit cell: (210.296, 185.364, 220.052, 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 8 26.01 S 72 16.00 P 1331 15.00 Mg 1 11.99 O 14103 8.00 N 10027 7.00 C 29720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.73 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 h 701 " pdb="FE4 SF4 h 701 " - pdb=" SG CYS h 58 " pdb="FE3 SF4 h 701 " - pdb=" SG CYS h 61 " pdb="FE2 SF4 h 701 " - pdb=" SG CYS h 55 " pdb="FE1 SF4 h 701 " - pdb=" SG CYS h 29 " pdb=" SF4 h 702 " pdb="FE2 SF4 h 702 " - pdb=" SG CYS h 21 " pdb="FE3 SF4 h 702 " - pdb=" SG CYS h 65 " pdb="FE1 SF4 h 702 " - pdb=" SG CYS h 25 " pdb="FE4 SF4 h 702 " - pdb=" SG CYS h 16 " Number of angles added : 24 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 36 sheets defined 27.8% alpha, 10.8% beta 347 base pairs and 637 stacking pairs defined. Time for finding SS restraints: 20.46 Creating SS restraints... Processing helix chain 'P' and resid 11 through 20 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 80 through 92 Processing helix chain 'P' and resid 130 through 138 removed outlier: 3.537A pdb=" N SER P 137 " --> pdb=" O ILE P 133 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR P 138 " --> pdb=" O LYS P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 183 Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 107 through 113 Processing helix chain 'Q' and resid 159 through 175 Processing helix chain 'Q' and resid 180 through 190 removed outlier: 3.750A pdb=" N LEU Q 184 " --> pdb=" O THR Q 180 " (cutoff:3.500A) Proline residue: Q 190 - end of helix Processing helix chain 'Q' and resid 193 through 203 removed outlier: 4.173A pdb=" N ASP Q 203 " --> pdb=" O ASN Q 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 Processing helix chain 'R' and resid 39 through 47 removed outlier: 4.469A pdb=" N ARG R 43 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 59 Processing helix chain 'R' and resid 67 through 72 removed outlier: 3.621A pdb=" N THR R 71 " --> pdb=" O GLN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 134 Processing helix chain 'R' and resid 182 through 191 Processing helix chain 'R' and resid 207 through 221 removed outlier: 4.218A pdb=" N LYS R 212 " --> pdb=" O GLU R 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 221 " --> pdb=" O ALA R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 229 No H-bonds generated for 'chain 'R' and resid 227 through 229' Processing helix chain 'R' and resid 239 through 242 No H-bonds generated for 'chain 'R' and resid 239 through 242' Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 44 through 49 Processing helix chain 'S' and resid 58 through 65 Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 118 through 120 No H-bonds generated for 'chain 'S' and resid 118 through 120' Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 248 through 254 Processing helix chain 'T' and resid 22 through 24 No H-bonds generated for 'chain 'T' and resid 22 through 24' Processing helix chain 'T' and resid 58 through 60 No H-bonds generated for 'chain 'T' and resid 58 through 60' Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 181 through 224 removed outlier: 3.699A pdb=" N GLU T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR T 208 " --> pdb=" O ALA T 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS T 223 " --> pdb=" O ARG T 219 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA T 224 " --> pdb=" O LYS T 220 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 9 No H-bonds generated for 'chain 'U' and resid 6 through 9' Processing helix chain 'U' and resid 15 through 28 Processing helix chain 'U' and resid 67 through 73 removed outlier: 3.723A pdb=" N LYS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 83 removed outlier: 3.512A pdb=" N LYS U 83 " --> pdb=" O ARG U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 116 No H-bonds generated for 'chain 'U' and resid 114 through 116' Processing helix chain 'U' and resid 118 through 129 Processing helix chain 'U' and resid 167 through 176 removed outlier: 3.628A pdb=" N GLN U 170 " --> pdb=" O GLU U 167 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA U 171 " --> pdb=" O SER U 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU U 176 " --> pdb=" O TYR U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 93 No H-bonds generated for 'chain 'V' and resid 90 through 93' Processing helix chain 'V' and resid 107 through 116 Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 154 through 162 Processing helix chain 'V' and resid 173 through 176 No H-bonds generated for 'chain 'V' and resid 173 through 176' Processing helix chain 'V' and resid 186 through 196 Processing helix chain 'W' and resid 21 through 34 removed outlier: 3.513A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS W 29 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 60 Processing helix chain 'W' and resid 67 through 83 removed outlier: 3.554A pdb=" N PHE W 71 " --> pdb=" O PRO W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 98 No H-bonds generated for 'chain 'W' and resid 95 through 98' Processing helix chain 'W' and resid 101 through 107 Processing helix chain 'W' and resid 109 through 116 removed outlier: 3.656A pdb=" N VAL W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 130 Processing helix chain 'W' and resid 153 through 155 No H-bonds generated for 'chain 'W' and resid 153 through 155' Processing helix chain 'W' and resid 172 through 177 Processing helix chain 'X' and resid 46 through 49 No H-bonds generated for 'chain 'X' and resid 46 through 49' Processing helix chain 'Y' and resid 31 through 43 Processing helix chain 'Y' and resid 47 through 56 Processing helix chain 'Y' and resid 63 through 66 No H-bonds generated for 'chain 'Y' and resid 63 through 66' Processing helix chain 'Y' and resid 71 through 78 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 110 through 131 removed outlier: 3.534A pdb=" N ARG Y 127 " --> pdb=" O HIS Y 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 150 Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 52 through 55 removed outlier: 4.001A pdb=" N SER Z 55 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 52 through 55' Processing helix chain 'Z' and resid 57 through 74 removed outlier: 3.573A pdb=" N LEU Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Z 65 " --> pdb=" O MET Z 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA Z 69 " --> pdb=" O GLN Z 65 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS Z 70 " --> pdb=" O ASP Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 106 removed outlier: 4.257A pdb=" N ALA Z 100 " --> pdb=" O PRO Z 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 62 Processing helix chain 'a' and resid 65 through 76 removed outlier: 3.545A pdb=" N ASP a 76 " --> pdb=" O LEU a 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 20 Processing helix chain 'b' and resid 32 through 44 removed outlier: 3.739A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 93 Processing helix chain 'b' and resid 113 through 119 Processing helix chain 'c' and resid 12 through 22 Processing helix chain 'c' and resid 27 through 33 Processing helix chain 'c' and resid 36 through 39 No H-bonds generated for 'chain 'c' and resid 36 through 39' Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'd' and resid 37 through 46 removed outlier: 4.256A pdb=" N ALA d 45 " --> pdb=" O ARG d 41 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU d 46 " --> pdb=" O GLU d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 85 Processing helix chain 'd' and resid 88 through 94 removed outlier: 3.728A pdb=" N VAL d 92 " --> pdb=" O THR d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 117 Processing helix chain 'd' and resid 123 through 132 Processing helix chain 'e' and resid 50 through 55 Processing helix chain 'e' and resid 76 through 80 Processing helix chain 'f' and resid 12 through 17 removed outlier: 3.651A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 17 Processing helix chain 'g' and resid 33 through 43 Processing helix chain 'h' and resid 18 through 21 No H-bonds generated for 'chain 'h' and resid 18 through 21' Processing helix chain 'h' and resid 24 through 27 No H-bonds generated for 'chain 'h' and resid 24 through 27' Processing helix chain 'h' and resid 32 through 34 No H-bonds generated for 'chain 'h' and resid 32 through 34' Processing helix chain 'h' and resid 60 through 63 No H-bonds generated for 'chain 'h' and resid 60 through 63' Processing helix chain 'h' and resid 116 through 124 Processing helix chain 'h' and resid 140 through 146 Processing helix chain 'h' and resid 151 through 161 removed outlier: 3.629A pdb=" N PHE h 156 " --> pdb=" O GLN h 153 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 179 removed outlier: 4.024A pdb=" N ARG h 178 " --> pdb=" O ASP h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 188 through 194 removed outlier: 3.634A pdb=" N LYS h 192 " --> pdb=" O GLY h 188 " (cutoff:3.500A) Processing helix chain 'h' and resid 200 through 208 Processing helix chain 'h' and resid 224 through 237 Processing helix chain 'h' and resid 254 through 267 removed outlier: 3.924A pdb=" N LEU h 258 " --> pdb=" O VAL h 254 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN h 259 " --> pdb=" O LYS h 255 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU h 267 " --> pdb=" O ILE h 263 " (cutoff:3.500A) Processing helix chain 'h' and resid 284 through 287 No H-bonds generated for 'chain 'h' and resid 284 through 287' Processing helix chain 'h' and resid 310 through 319 removed outlier: 3.749A pdb=" N ASP h 319 " --> pdb=" O ASN h 315 " (cutoff:3.500A) Processing helix chain 'h' and resid 391 through 399 removed outlier: 3.833A pdb=" N ILE h 395 " --> pdb=" O LYS h 391 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 436 removed outlier: 4.002A pdb=" N LYS h 436 " --> pdb=" O GLN h 432 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 450 No H-bonds generated for 'chain 'h' and resid 447 through 450' Processing helix chain 'h' and resid 458 through 461 No H-bonds generated for 'chain 'h' and resid 458 through 461' Processing helix chain 'h' and resid 470 through 479 Processing helix chain 'h' and resid 500 through 516 removed outlier: 3.746A pdb=" N ILE h 504 " --> pdb=" O SER h 500 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE h 505 " --> pdb=" O GLU h 501 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS h 506 " --> pdb=" O GLN h 502 " (cutoff:3.500A) Processing helix chain 'h' and resid 528 through 532 Processing helix chain 'h' and resid 557 through 568 removed outlier: 3.768A pdb=" N ASN h 567 " --> pdb=" O ARG h 563 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU h 568 " --> pdb=" O PHE h 564 " (cutoff:3.500A) Processing helix chain 'h' and resid 589 through 597 removed outlier: 3.526A pdb=" N GLU h 593 " --> pdb=" O GLN h 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'P' and resid 74 through 76 removed outlier: 7.785A pdb=" N VAL P 123 " --> pdb=" O PRO P 142 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE P 144 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 37 through 41 removed outlier: 3.540A pdb=" N VAL P 47 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA P 40 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL P 45 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'Q' and resid 65 through 69 Processing sheet with id= D, first strand: chain 'Q' and resid 124 through 128 Processing sheet with id= E, first strand: chain 'Q' and resid 29 through 33 Processing sheet with id= F, first strand: chain 'R' and resid 81 through 89 removed outlier: 4.014A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 158 through 162 Processing sheet with id= H, first strand: chain 'S' and resid 89 through 91 Processing sheet with id= I, first strand: chain 'S' and resid 122 through 125 removed outlier: 3.593A pdb=" N THR S 159 " --> pdb=" O ILE S 173 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 128 through 131 removed outlier: 3.872A pdb=" N LYS S 128 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 207 through 211 Processing sheet with id= L, first strand: chain 'T' and resid 12 through 17 removed outlier: 3.689A pdb=" N LEU T 109 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'T' and resid 72 through 77 Processing sheet with id= O, first strand: chain 'U' and resid 46 through 50 Processing sheet with id= P, first strand: chain 'U' and resid 180 through 185 removed outlier: 3.949A pdb=" N GLN U 180 " --> pdb=" O LYS U 148 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 42 through 46 Processing sheet with id= R, first strand: chain 'V' and resid 62 through 66 Processing sheet with id= S, first strand: chain 'V' and resid 181 through 183 removed outlier: 3.908A pdb=" N ALA V 100 " --> pdb=" O ILE V 169 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 99 through 110 removed outlier: 3.627A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 14.161A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 16.766A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 22.639A pdb=" N TYR X 93 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 26.250A pdb=" N GLY X 68 " --> pdb=" O TYR X 93 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS X 69 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL X 125 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU X 71 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL X 123 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY X 126 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL X 139 " --> pdb=" O GLY X 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Z' and resid 80 through 83 removed outlier: 5.828A pdb=" N ARG Z 114 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE Z 83 " --> pdb=" O ARG Z 114 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU Z 116 " --> pdb=" O ILE Z 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'a' and resid 32 through 37 Processing sheet with id= W, first strand: chain 'b' and resid 24 through 27 Processing sheet with id= X, first strand: chain 'b' and resid 71 through 73 Processing sheet with id= Y, first strand: chain 'c' and resid 54 through 56 Processing sheet with id= Z, first strand: chain 'd' and resid 13 through 15 Processing sheet with id= AA, first strand: chain 'd' and resid 60 through 62 Processing sheet with id= AB, first strand: chain 'd' and resid 5 through 10 removed outlier: 4.648A pdb=" N ILE d 7 " --> pdb=" O ASP d 26 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP d 26 " --> pdb=" O ILE d 7 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR d 9 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL d 24 " --> pdb=" O THR d 9 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 20 through 22 Processing sheet with id= AD, first strand: chain 'e' and resid 38 through 43 Processing sheet with id= AE, first strand: chain 'f' and resid 32 through 35 Processing sheet with id= AF, first strand: chain 'h' and resid 6 through 10 removed outlier: 3.761A pdb=" N SER h 6 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'h' and resid 242 through 246 removed outlier: 6.380A pdb=" N TYR h 273 " --> pdb=" O TYR h 243 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE h 245 " --> pdb=" O TYR h 273 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE h 275 " --> pdb=" O PHE h 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'h' and resid 294 through 297 Processing sheet with id= AI, first strand: chain 'h' and resid 360 through 362 removed outlier: 3.722A pdb=" N ALA h 551 " --> pdb=" O ASN h 369 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL h 540 " --> pdb=" O ARG h 552 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ILE h 539 " --> pdb=" O ILE h 380 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL h 382 " --> pdb=" O ILE h 539 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE h 541 " --> pdb=" O VAL h 382 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET h 384 " --> pdb=" O PHE h 541 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA h 521 " --> pdb=" O GLU h 379 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'h' and resid 572 through 574 683 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 842 hydrogen bonds 1434 hydrogen bond angles 0 basepair planarities 347 basepair parallelities 637 stacking parallelities Total time for adding SS restraints: 28.40 Time building geometry restraints manager: 22.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.36: 15282 1.36 - 1.65: 43685 1.65 - 1.94: 99 1.94 - 2.23: 24 2.23 - 2.52: 2 Bond restraints: 59092 Sorted by residual: bond pdb=" CG ASP h 14 " pdb=" OD1 ASP h 14 " ideal model delta sigma weight residual 1.249 2.520 -1.271 1.90e-02 2.77e+03 4.48e+03 bond pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 1.249 2.401 -1.152 1.90e-02 2.77e+03 3.68e+03 bond pdb=" O3' U 21761 " pdb=" P A 21762 " ideal model delta sigma weight residual 1.607 1.070 0.537 1.50e-02 4.44e+03 1.28e+03 bond pdb=" O3' C 21636 " pdb=" P C 21637 " ideal model delta sigma weight residual 1.607 1.241 0.366 1.50e-02 4.44e+03 5.96e+02 bond pdb=" CA ARG h 101 " pdb=" C ARG h 101 " ideal model delta sigma weight residual 1.524 1.724 -0.200 1.26e-02 6.30e+03 2.53e+02 ... (remaining 59087 not shown) Histogram of bond angle deviations from ideal: 33.91 - 54.66: 3 54.66 - 75.42: 1 75.42 - 96.18: 47 96.18 - 116.93: 51002 116.93 - 137.69: 35211 Bond angle restraints: 86264 Sorted by residual: angle pdb=" CB ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 118.40 33.91 84.49 2.30e+00 1.89e-01 1.35e+03 angle pdb=" OD1 ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD2 ASP h 14 " ideal model delta sigma weight residual 122.90 52.95 69.95 2.40e+00 1.74e-01 8.49e+02 angle pdb=" CB ASP h 14 " pdb=" CG ASP h 14 " pdb=" OD1 ASP h 14 " ideal model delta sigma weight residual 118.40 51.77 66.63 2.30e+00 1.89e-01 8.39e+02 angle pdb=" CA THR h 99 " pdb=" C THR h 99 " pdb=" N PRO h 100 " ideal model delta sigma weight residual 118.44 74.68 43.76 1.59e+00 3.96e-01 7.57e+02 angle pdb="FE2 SF4 h 701 " pdb=" S4 SF4 h 701 " pdb="FE3 SF4 h 701 " ideal model delta sigma weight residual 73.70 100.56 -26.86 1.50e+00 4.44e-01 3.21e+02 ... (remaining 86259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 33517 35.83 - 71.66: 3379 71.66 - 107.49: 409 107.49 - 143.32: 28 143.32 - 179.15: 34 Dihedral angle restraints: 37367 sinusoidal: 27484 harmonic: 9883 Sorted by residual: dihedral pdb=" C5' U 2 128 " pdb=" C4' U 2 128 " pdb=" C3' U 2 128 " pdb=" O3' U 2 128 " ideal model delta sinusoidal sigma weight residual 147.00 73.35 73.65 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C5' U 2 159 " pdb=" C4' U 2 159 " pdb=" C3' U 2 159 " pdb=" O3' U 2 159 " ideal model delta sinusoidal sigma weight residual 147.00 73.81 73.19 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C5' U 2 721 " pdb=" C4' U 2 721 " pdb=" C3' U 2 721 " pdb=" O3' U 2 721 " ideal model delta sinusoidal sigma weight residual 147.00 74.39 72.61 1 8.00e+00 1.56e-02 1.05e+02 ... (remaining 37364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 10402 0.222 - 0.443: 362 0.443 - 0.665: 20 0.665 - 0.887: 9 0.887 - 1.109: 3 Chirality restraints: 10796 Sorted by residual: chirality pdb="FE3 SF4 h 701 " pdb=" S1 SF4 h 701 " pdb=" S2 SF4 h 701 " pdb=" S4 SF4 h 701 " both_signs ideal model delta sigma weight residual False -10.55 -9.45 -1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb="FE2 SF4 h 701 " pdb=" S1 SF4 h 701 " pdb=" S3 SF4 h 701 " pdb=" S4 SF4 h 701 " both_signs ideal model delta sigma weight residual False 10.55 9.59 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb="FE2 SF4 h 702 " pdb=" S1 SF4 h 702 " pdb=" S3 SF4 h 702 " pdb=" S4 SF4 h 702 " both_signs ideal model delta sigma weight residual False 10.55 9.66 0.89 2.00e-01 2.50e+01 2.00e+01 ... (remaining 10793 not shown) Planarity restraints: 6060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP h 14 " -0.572 2.00e-02 2.50e+03 3.43e-01 1.18e+03 pdb=" CG ASP h 14 " 0.255 2.00e-02 2.50e+03 pdb=" OD1 ASP h 14 " 0.037 2.00e-02 2.50e+03 pdb=" OD2 ASP h 14 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR h 99 " -0.014 2.00e-02 2.50e+03 1.94e-01 3.76e+02 pdb=" C THR h 99 " 0.319 2.00e-02 2.50e+03 pdb=" O THR h 99 " -0.180 2.00e-02 2.50e+03 pdb=" N PRO h 100 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 8 " 0.042 2.00e-02 2.50e+03 9.24e-02 1.92e+02 pdb=" N1 U 2 8 " -0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 8 " -0.017 2.00e-02 2.50e+03 pdb=" O2 U 2 8 " -0.114 2.00e-02 2.50e+03 pdb=" N3 U 2 8 " 0.215 2.00e-02 2.50e+03 pdb=" C4 U 2 8 " 0.042 2.00e-02 2.50e+03 pdb=" O4 U 2 8 " -0.109 2.00e-02 2.50e+03 pdb=" C5 U 2 8 " -0.026 2.00e-02 2.50e+03 pdb=" C6 U 2 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 6057 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.72: 19 1.72 - 2.51: 197 2.51 - 3.31: 59522 3.31 - 4.10: 158377 4.10 - 4.90: 245614 Warning: very small nonbonded interaction distances. Nonbonded interactions: 463729 Sorted by model distance: nonbonded pdb=" N1 A 21116 " pdb=" C4 A 21131 " model vdw 0.924 3.340 nonbonded pdb=" C2 A 21116 " pdb=" N1 A 21131 " model vdw 1.191 3.420 nonbonded pdb=" N1 A 21116 " pdb=" C5 A 21131 " model vdw 1.191 3.340 nonbonded pdb=" CA ARG h 148 " pdb=" NE2 GLN h 153 " model vdw 1.194 3.550 nonbonded pdb=" OP1 C 21674 " pdb=" NH1 ARG T 92 " model vdw 1.211 2.520 ... (remaining 463724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.060 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: 0.050 Extract box with map and model: 13.250 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 138.030 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.012 1.271 59092 Z= 0.639 Angle : 1.502 84.493 86264 Z= 0.945 Chirality : 0.108 1.109 10796 Planarity : 0.010 0.343 6060 Dihedral : 23.627 179.146 30983 Min Nonbonded Distance : 0.924 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 3.66 % Allowed : 10.63 % Favored : 85.71 % Rotamer: Outliers : 2.53 % Allowed : 7.37 % Favored : 90.10 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 3387 helix: -0.98 (0.15), residues: 956 sheet: -3.34 (0.17), residues: 545 loop : -3.30 (0.12), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP a 83 HIS 0.011 0.003 HIS Y 123 PHE 0.053 0.004 PHE h 230 TYR 0.040 0.005 TYR X 97 ARG 0.023 0.002 ARG R 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1174 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 8 ASP cc_start: 0.8717 (m-30) cc_final: 0.8477 (m-30) REVERT: P 16 LEU cc_start: 0.8317 (mt) cc_final: 0.8072 (mt) REVERT: P 39 ASN cc_start: 0.8037 (m-40) cc_final: 0.7832 (t0) REVERT: P 41 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.6624 (mmt180) REVERT: P 50 VAL cc_start: 0.9247 (t) cc_final: 0.9032 (p) REVERT: P 52 LYS cc_start: 0.8629 (mttt) cc_final: 0.8417 (mttp) REVERT: P 55 GLU cc_start: 0.9131 (tt0) cc_final: 0.8555 (tp30) REVERT: P 57 LEU cc_start: 0.9542 (tt) cc_final: 0.9324 (tt) REVERT: P 84 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7250 (ttm-80) REVERT: P 110 TYR cc_start: 0.7714 (p90) cc_final: 0.7454 (p90) REVERT: P 197 ILE cc_start: 0.8143 (mp) cc_final: 0.7911 (mm) REVERT: Q 24 PHE cc_start: 0.8149 (m-80) cc_final: 0.7944 (t80) REVERT: Q 31 ASP cc_start: 0.7411 (p0) cc_final: 0.7166 (p0) REVERT: Q 73 LEU cc_start: 0.8043 (pp) cc_final: 0.7807 (tp) REVERT: Q 74 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7195 (tm-30) REVERT: Q 76 SER cc_start: 0.8213 (t) cc_final: 0.7723 (t) REVERT: Q 83 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7701 (mtmt) REVERT: Q 111 ARG cc_start: 0.8408 (mmt90) cc_final: 0.8139 (mpt180) REVERT: Q 112 SER cc_start: 0.7847 (t) cc_final: 0.7569 (p) REVERT: Q 132 ASP cc_start: 0.7960 (t0) cc_final: 0.7576 (t0) REVERT: Q 133 TYR cc_start: 0.7354 (m-80) cc_final: 0.6917 (m-80) REVERT: Q 144 ARG cc_start: 0.8535 (ptt90) cc_final: 0.7893 (ptt180) REVERT: Q 165 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8422 (ttm110) REVERT: Q 183 GLN cc_start: 0.9072 (mm110) cc_final: 0.8686 (pp30) REVERT: Q 184 LEU cc_start: 0.9352 (mt) cc_final: 0.8691 (mt) REVERT: Q 229 MET cc_start: 0.8129 (mmm) cc_final: 0.7631 (mtt) REVERT: R 66 PHE cc_start: 0.8650 (p90) cc_final: 0.8385 (p90) REVERT: R 67 GLN cc_start: 0.8658 (mp10) cc_final: 0.8344 (mt0) REVERT: R 70 ASP cc_start: 0.8872 (m-30) cc_final: 0.8467 (m-30) REVERT: R 106 ASP cc_start: 0.8760 (p0) cc_final: 0.8402 (p0) REVERT: R 107 SER cc_start: 0.9094 (m) cc_final: 0.8761 (p) REVERT: R 193 VAL cc_start: 0.9175 (t) cc_final: 0.8739 (p) REVERT: R 230 TRP cc_start: 0.9148 (m-10) cc_final: 0.8733 (m-10) REVERT: R 233 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8156 (mm-40) REVERT: S 37 LYS cc_start: 0.8925 (mttm) cc_final: 0.8569 (mmtt) REVERT: S 89 VAL cc_start: 0.9259 (t) cc_final: 0.8976 (m) REVERT: S 104 ASP cc_start: 0.9013 (m-30) cc_final: 0.8633 (t70) REVERT: S 163 ASP cc_start: 0.8840 (t70) cc_final: 0.8469 (t70) REVERT: S 176 ASP cc_start: 0.7368 (t0) cc_final: 0.7005 (t0) REVERT: S 200 ARG cc_start: 0.8699 (ttt180) cc_final: 0.8183 (ttm170) REVERT: S 211 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8309 (pttm) REVERT: S 212 ASP cc_start: 0.8613 (p0) cc_final: 0.8373 (p0) REVERT: S 214 LEU cc_start: 0.9363 (mp) cc_final: 0.8722 (tp) REVERT: S 215 ASP cc_start: 0.9109 (m-30) cc_final: 0.8875 (m-30) REVERT: S 216 ASN cc_start: 0.9225 (m-40) cc_final: 0.8874 (m-40) REVERT: S 223 ASN cc_start: 0.9087 (t0) cc_final: 0.8849 (m-40) REVERT: T 19 ASP cc_start: 0.9026 (m-30) cc_final: 0.8803 (m-30) REVERT: T 20 ASP cc_start: 0.8636 (m-30) cc_final: 0.8075 (t70) REVERT: T 21 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8485 (pm20) REVERT: T 23 ARG cc_start: 0.9058 (ttm-80) cc_final: 0.8828 (mmp80) REVERT: T 125 THR cc_start: 0.9245 (m) cc_final: 0.9005 (p) REVERT: T 201 GLN cc_start: 0.8706 (mm110) cc_final: 0.7723 (tm-30) REVERT: U 9 LEU cc_start: 0.5052 (tt) cc_final: 0.4796 (tp) REVERT: U 80 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8478 (mp0) REVERT: U 83 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8897 (ttpt) REVERT: V 94 ASN cc_start: 0.8952 (m-40) cc_final: 0.8681 (m-40) REVERT: V 114 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8295 (pt0) REVERT: V 153 GLU cc_start: 0.8019 (tt0) cc_final: 0.7771 (tt0) REVERT: V 182 TYR cc_start: 0.8242 (p90) cc_final: 0.7949 (p90) REVERT: V 185 GLU cc_start: 0.8178 (tt0) cc_final: 0.7707 (pp20) REVERT: V 189 LEU cc_start: 0.9018 (tp) cc_final: 0.8801 (tp) REVERT: W 6 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8755 (mtp85) REVERT: W 16 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7584 (mmtt) REVERT: W 72 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8593 (mp0) REVERT: W 91 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8533 (ttmm) REVERT: W 112 GLN cc_start: 0.9079 (mm110) cc_final: 0.8771 (mm110) REVERT: X 53 TYR cc_start: 0.7755 (p90) cc_final: 0.7485 (p90) REVERT: X 55 ASP cc_start: 0.8953 (t0) cc_final: 0.8707 (t0) REVERT: X 70 ILE cc_start: 0.8683 (mp) cc_final: 0.8445 (mm) REVERT: X 96 LYS cc_start: 0.9109 (tptm) cc_final: 0.8877 (tttt) REVERT: X 138 ASN cc_start: 0.8611 (t0) cc_final: 0.8326 (t0) REVERT: Y 62 GLN cc_start: 0.7133 (mt0) cc_final: 0.6760 (mt0) REVERT: Y 76 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8500 (ttpp) REVERT: Y 105 ASN cc_start: 0.7881 (m-40) cc_final: 0.7474 (p0) REVERT: Y 107 LYS cc_start: 0.8802 (tptp) cc_final: 0.8446 (tttt) REVERT: Y 134 VAL cc_start: 0.8737 (m) cc_final: 0.8418 (p) REVERT: Z 19 ILE cc_start: 0.8964 (mt) cc_final: 0.8744 (pt) REVERT: Z 93 THR cc_start: 0.8265 (m) cc_final: 0.7945 (p) REVERT: Z 118 VAL cc_start: 0.6782 (m) cc_final: 0.6317 (m) REVERT: a 64 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7412 (tp30) REVERT: a 78 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8403 (pt) REVERT: b 24 GLN cc_start: 0.9293 (pm20) cc_final: 0.9028 (pm20) REVERT: b 50 PHE cc_start: 0.9285 (p90) cc_final: 0.9022 (p90) REVERT: b 68 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8442 (mtt90) REVERT: b 97 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8508 (mtp85) REVERT: b 98 GLN cc_start: 0.8299 (pm20) cc_final: 0.8074 (mp10) REVERT: b 101 TYR cc_start: 0.8896 (m-80) cc_final: 0.8481 (m-80) REVERT: b 112 ASP cc_start: 0.9436 (p0) cc_final: 0.9050 (p0) REVERT: b 120 HIS cc_start: 0.8591 (t-90) cc_final: 0.8287 (m-70) REVERT: c 23 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8207 (mtp85) REVERT: c 24 TRP cc_start: 0.8866 (m100) cc_final: 0.8581 (m-10) REVERT: c 34 LEU cc_start: 0.9104 (mt) cc_final: 0.8850 (mt) REVERT: c 52 ILE cc_start: 0.8595 (mt) cc_final: 0.8351 (mm) REVERT: d 6 THR cc_start: 0.8762 (m) cc_final: 0.8506 (p) REVERT: d 26 ASP cc_start: 0.8648 (t0) cc_final: 0.8204 (t0) REVERT: d 34 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8276 (t0) REVERT: d 57 VAL cc_start: 0.6242 (OUTLIER) cc_final: 0.6016 (p) REVERT: d 74 LEU cc_start: 0.8213 (mt) cc_final: 0.7904 (mt) REVERT: d 84 LYS cc_start: 0.9135 (ptmt) cc_final: 0.8907 (tppt) REVERT: d 94 TYR cc_start: 0.7822 (m-10) cc_final: 0.7614 (m-80) REVERT: d 98 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8267 (mm-30) REVERT: f 22 LYS cc_start: 0.9129 (mttt) cc_final: 0.8808 (mttm) REVERT: f 33 LEU cc_start: 0.8234 (pp) cc_final: 0.7976 (mt) REVERT: f 42 ASN cc_start: 0.8053 (m110) cc_final: 0.7738 (m-40) REVERT: f 47 PHE cc_start: 0.7449 (t80) cc_final: 0.7180 (t80) REVERT: g 3 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7119 (mmtp) REVERT: g 10 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7604 (mpp80) REVERT: g 20 LYS cc_start: 0.8287 (tptp) cc_final: 0.8071 (tptt) REVERT: g 35 TYR cc_start: 0.8642 (t80) cc_final: 0.7863 (t80) REVERT: g 44 PHE cc_start: 0.8483 (m-80) cc_final: 0.8068 (m-80) REVERT: h 53 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8111 (tp) REVERT: h 151 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7885 (pm20) REVERT: h 161 GLU cc_start: 0.8461 (tt0) cc_final: 0.8136 (tt0) REVERT: h 198 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.7806 (p) REVERT: h 246 ASP cc_start: 0.8382 (t0) cc_final: 0.7943 (t0) REVERT: h 247 GLU cc_start: 0.8538 (tp30) cc_final: 0.8229 (tp30) REVERT: h 321 HIS cc_start: 0.6756 (p-80) cc_final: 0.6467 (t70) REVERT: h 379 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7236 (mm-30) REVERT: h 499 ASP cc_start: 0.8134 (p0) cc_final: 0.7485 (p0) REVERT: h 556 SER cc_start: 0.7250 (t) cc_final: 0.6761 (t) REVERT: h 564 PHE cc_start: 0.8816 (t80) cc_final: 0.8491 (t80) REVERT: h 573 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7385 (ttm110) outliers start: 73 outliers final: 14 residues processed: 1220 average time/residue: 0.6536 time to fit residues: 1289.6988 Evaluate side-chains 770 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 750 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain d residue 34 ASN Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 114 ILE Chi-restraints excluded: chain h residue 138 PRO Chi-restraints excluded: chain h residue 153 GLN Chi-restraints excluded: chain h residue 198 SER Chi-restraints excluded: chain h residue 209 LEU Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 273 TYR Chi-restraints excluded: chain h residue 426 PHE Chi-restraints excluded: chain h residue 573 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 HIS P 69 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 ASN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS S 98 ASN S 142 HIS S 153 ASN T 22 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN V 103 GLN V 116 HIS V 119 GLN W 110 GLN W 176 ASN X 8 GLN X 118 GLN a 7 GLN a 81 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 27 ASN d 22 GLN d 106 GLN d 107 GLN d 110 GLN e 11 ASN g 17 GLN h 5 ASN h 326 ASN h 363 GLN h 446 GLN h 562 ASN h 584 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 59092 Z= 0.206 Angle : 0.740 12.936 86264 Z= 0.378 Chirality : 0.042 0.314 10796 Planarity : 0.006 0.076 6060 Dihedral : 24.229 179.421 24238 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 1.21 % Allowed : 9.80 % Favored : 88.99 % Rotamer: Outliers : 5.37 % Allowed : 17.83 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3387 helix: 0.37 (0.17), residues: 978 sheet: -2.43 (0.18), residues: 587 loop : -3.05 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 24 HIS 0.006 0.001 HIS U 89 PHE 0.027 0.002 PHE b 99 TYR 0.024 0.002 TYR P 202 ARG 0.011 0.001 ARG S 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 855 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 41 ARG cc_start: 0.7209 (ttp-170) cc_final: 0.6561 (mmt180) REVERT: P 102 PHE cc_start: 0.8805 (t80) cc_final: 0.8536 (t80) REVERT: P 107 PHE cc_start: 0.8863 (m-80) cc_final: 0.8396 (m-80) REVERT: P 128 SER cc_start: 0.8569 (m) cc_final: 0.8251 (t) REVERT: P 148 ASP cc_start: 0.8175 (t0) cc_final: 0.7854 (t0) REVERT: P 150 ASP cc_start: 0.8655 (p0) cc_final: 0.8373 (p0) REVERT: P 197 ILE cc_start: 0.8002 (mp) cc_final: 0.7784 (mm) REVERT: Q 74 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7111 (tm-30) REVERT: Q 76 SER cc_start: 0.8219 (t) cc_final: 0.7717 (t) REVERT: Q 83 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7977 (pttt) REVERT: Q 89 ASP cc_start: 0.7390 (m-30) cc_final: 0.6909 (p0) REVERT: Q 136 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5966 (mtp-110) REVERT: Q 149 GLN cc_start: 0.8914 (tp40) cc_final: 0.8569 (tp40) REVERT: Q 165 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8627 (ttm110) REVERT: Q 184 LEU cc_start: 0.9314 (mt) cc_final: 0.8747 (mt) REVERT: Q 203 ASP cc_start: 0.8223 (m-30) cc_final: 0.7978 (m-30) REVERT: Q 229 MET cc_start: 0.7938 (mmm) cc_final: 0.7537 (mtt) REVERT: R 54 GLU cc_start: 0.8809 (mp0) cc_final: 0.8562 (pm20) REVERT: R 76 LEU cc_start: 0.7816 (mp) cc_final: 0.7531 (tt) REVERT: R 116 LYS cc_start: 0.8816 (tptt) cc_final: 0.8555 (tppt) REVERT: S 89 VAL cc_start: 0.9366 (t) cc_final: 0.9018 (m) REVERT: S 198 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8529 (ttmt) REVERT: S 200 ARG cc_start: 0.8607 (ttt180) cc_final: 0.8197 (tpp-160) REVERT: S 207 LEU cc_start: 0.9315 (mt) cc_final: 0.8829 (mp) REVERT: S 211 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8149 (pttm) REVERT: S 214 LEU cc_start: 0.9423 (mp) cc_final: 0.8869 (tp) REVERT: S 216 ASN cc_start: 0.9070 (m-40) cc_final: 0.8731 (m-40) REVERT: S 223 ASN cc_start: 0.8862 (t0) cc_final: 0.8642 (m-40) REVERT: T 20 ASP cc_start: 0.8742 (m-30) cc_final: 0.7866 (t70) REVERT: T 21 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8392 (pm20) REVERT: T 201 GLN cc_start: 0.8803 (mm110) cc_final: 0.7548 (tm-30) REVERT: T 210 GLN cc_start: 0.7012 (mt0) cc_final: 0.6510 (tm-30) REVERT: U 49 ILE cc_start: 0.7651 (tp) cc_final: 0.7434 (tp) REVERT: U 83 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8791 (tppt) REVERT: U 127 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7925 (mm-30) REVERT: V 74 LYS cc_start: 0.7813 (mmtt) cc_final: 0.6737 (mtmm) REVERT: V 89 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7467 (mm-30) REVERT: V 114 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8067 (mm-30) REVERT: V 168 CYS cc_start: 0.8228 (t) cc_final: 0.7718 (t) REVERT: V 182 TYR cc_start: 0.8411 (p90) cc_final: 0.7631 (p90) REVERT: V 185 GLU cc_start: 0.8243 (tt0) cc_final: 0.7935 (pp20) REVERT: V 189 LEU cc_start: 0.9141 (tp) cc_final: 0.8891 (tp) REVERT: W 63 ASP cc_start: 0.9017 (t0) cc_final: 0.8806 (t0) REVERT: W 72 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8587 (mp0) REVERT: W 91 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8377 (mttp) REVERT: W 174 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7969 (ttp80) REVERT: X 50 GLU cc_start: 0.8305 (tp30) cc_final: 0.8016 (mm-30) REVERT: X 55 ASP cc_start: 0.7972 (t0) cc_final: 0.7691 (t0) REVERT: X 97 TYR cc_start: 0.9047 (m-80) cc_final: 0.8446 (m-80) REVERT: Y 105 ASN cc_start: 0.7995 (m-40) cc_final: 0.7626 (p0) REVERT: Y 134 VAL cc_start: 0.8679 (m) cc_final: 0.8340 (p) REVERT: a 4 ASP cc_start: 0.8574 (t0) cc_final: 0.8343 (p0) REVERT: a 21 ASN cc_start: 0.9603 (m-40) cc_final: 0.9385 (t0) REVERT: a 64 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7388 (tp30) REVERT: a 69 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8610 (tt) REVERT: b 24 GLN cc_start: 0.9288 (pm20) cc_final: 0.8823 (pm20) REVERT: b 42 GLN cc_start: 0.8904 (tt0) cc_final: 0.8685 (tt0) REVERT: b 54 ASP cc_start: 0.8950 (t0) cc_final: 0.8728 (t0) REVERT: b 98 GLN cc_start: 0.8174 (pm20) cc_final: 0.7973 (mp10) REVERT: b 112 ASP cc_start: 0.9331 (p0) cc_final: 0.8992 (p0) REVERT: c 34 LEU cc_start: 0.9187 (mt) cc_final: 0.8975 (mt) REVERT: c 120 VAL cc_start: 0.9154 (p) cc_final: 0.8910 (p) REVERT: c 140 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8728 (mmmt) REVERT: d 6 THR cc_start: 0.8586 (m) cc_final: 0.8374 (p) REVERT: d 26 ASP cc_start: 0.8500 (t0) cc_final: 0.8010 (t0) REVERT: d 84 LYS cc_start: 0.9055 (ptmt) cc_final: 0.8782 (tppt) REVERT: f 22 LYS cc_start: 0.9228 (mttt) cc_final: 0.9025 (mttm) REVERT: f 54 VAL cc_start: 0.8059 (t) cc_final: 0.7853 (p) REVERT: g 3 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7054 (mmtp) REVERT: g 20 LYS cc_start: 0.8029 (tptp) cc_final: 0.7683 (mtmm) REVERT: g 25 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7827 (pp20) REVERT: g 35 TYR cc_start: 0.8567 (t80) cc_final: 0.7798 (t80) REVERT: h 5 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8074 (m-40) REVERT: h 74 ASN cc_start: 0.7615 (p0) cc_final: 0.6640 (p0) REVERT: h 152 LEU cc_start: 0.8102 (mt) cc_final: 0.7723 (mt) REVERT: h 161 GLU cc_start: 0.8460 (tt0) cc_final: 0.8120 (tt0) REVERT: h 171 GLN cc_start: 0.6568 (tp40) cc_final: 0.6305 (tp40) REVERT: h 174 ASP cc_start: 0.5805 (t70) cc_final: 0.5054 (t0) REVERT: h 197 LYS cc_start: 0.7923 (tptt) cc_final: 0.7625 (ttmm) REVERT: h 198 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7588 (m) REVERT: h 202 VAL cc_start: 0.8893 (m) cc_final: 0.8480 (p) REVERT: h 205 TYR cc_start: 0.8716 (m-10) cc_final: 0.7964 (m-80) REVERT: h 226 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7384 (mp0) REVERT: h 246 ASP cc_start: 0.8449 (t0) cc_final: 0.8050 (t0) REVERT: h 492 ASP cc_start: 0.6823 (t0) cc_final: 0.6033 (p0) REVERT: h 499 ASP cc_start: 0.8238 (p0) cc_final: 0.7740 (p0) REVERT: h 507 SER cc_start: 0.6429 (OUTLIER) cc_final: 0.5714 (t) REVERT: h 536 ASP cc_start: 0.5965 (t70) cc_final: 0.5634 (t70) outliers start: 155 outliers final: 76 residues processed: 941 average time/residue: 0.5628 time to fit residues: 867.8833 Evaluate side-chains 795 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 713 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 168 HIS Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 136 ARG Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 185 LYS Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 198 LYS Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 LEU Chi-restraints excluded: chain T residue 133 LEU Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 107 ARG Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain h residue 5 ASN Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 121 LYS Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 198 SER Chi-restraints excluded: chain h residue 209 LEU Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 426 PHE Chi-restraints excluded: chain h residue 507 SER Chi-restraints excluded: chain h residue 537 LYS Chi-restraints excluded: chain h residue 538 VAL Chi-restraints excluded: chain h residue 570 VAL Chi-restraints excluded: chain h residue 584 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 458 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 421 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 23 HIS P 33 GLN P 83 GLN P 92 HIS ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 HIS Q 49 ASN Q 74 GLN Q 101 HIS ** Q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN R 209 ASN ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 HIS T 4 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 GLN T 182 GLN ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 116 HIS V 159 GLN ** W 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN a 21 ASN a 29 HIS a 81 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN d 63 GLN e 72 HIS f 26 GLN f 42 ASN f 49 HIS h 228 GLN h 326 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 59092 Z= 0.459 Angle : 0.903 13.840 86264 Z= 0.455 Chirality : 0.048 0.287 10796 Planarity : 0.007 0.132 6060 Dihedral : 24.391 179.083 24215 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 1.09 % Allowed : 12.43 % Favored : 86.48 % Rotamer: Outliers : 7.75 % Allowed : 20.08 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3387 helix: -0.29 (0.16), residues: 966 sheet: -2.43 (0.19), residues: 574 loop : -2.98 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP c 136 HIS 0.010 0.002 HIS X 81 PHE 0.048 0.003 PHE S 205 TYR 0.025 0.003 TYR h 301 ARG 0.017 0.001 ARG Q 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 727 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 ASN cc_start: 0.7591 (m-40) cc_final: 0.7001 (t0) REVERT: P 41 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.6663 (mmt180) REVERT: P 88 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8654 (mmmm) REVERT: P 107 PHE cc_start: 0.8981 (m-80) cc_final: 0.8490 (m-80) REVERT: P 148 ASP cc_start: 0.8491 (t0) cc_final: 0.8017 (t0) REVERT: P 150 ASP cc_start: 0.8790 (p0) cc_final: 0.8473 (p0) REVERT: P 163 ASN cc_start: 0.8568 (t0) cc_final: 0.8277 (t0) REVERT: Q 66 VAL cc_start: 0.8411 (t) cc_final: 0.8084 (m) REVERT: Q 73 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7698 (pp) REVERT: Q 74 GLN cc_start: 0.7940 (tp40) cc_final: 0.7169 (tm-30) REVERT: Q 76 SER cc_start: 0.8383 (t) cc_final: 0.7807 (t) REVERT: Q 83 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7742 (mtmt) REVERT: Q 89 ASP cc_start: 0.7712 (m-30) cc_final: 0.7117 (p0) REVERT: Q 165 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8354 (ttm110) REVERT: Q 179 SER cc_start: 0.8340 (t) cc_final: 0.8063 (m) REVERT: Q 229 MET cc_start: 0.7926 (mmm) cc_final: 0.7671 (mtt) REVERT: R 54 GLU cc_start: 0.8973 (mp0) cc_final: 0.8701 (pm20) REVERT: R 193 VAL cc_start: 0.9361 (t) cc_final: 0.9024 (p) REVERT: R 230 TRP cc_start: 0.9133 (m-10) cc_final: 0.8912 (m-10) REVERT: R 238 SER cc_start: 0.7593 (OUTLIER) cc_final: 0.7113 (p) REVERT: R 244 SER cc_start: 0.8247 (t) cc_final: 0.7912 (p) REVERT: S 89 VAL cc_start: 0.9526 (t) cc_final: 0.9228 (m) REVERT: S 106 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8579 (mttm) REVERT: S 200 ARG cc_start: 0.8551 (ttt180) cc_final: 0.8111 (tpp-160) REVERT: S 214 LEU cc_start: 0.9481 (mp) cc_final: 0.9051 (tp) REVERT: S 216 ASN cc_start: 0.9088 (m-40) cc_final: 0.8745 (m-40) REVERT: S 223 ASN cc_start: 0.8957 (t0) cc_final: 0.8724 (m-40) REVERT: T 20 ASP cc_start: 0.9101 (m-30) cc_final: 0.8080 (t0) REVERT: T 21 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8860 (pm20) REVERT: T 23 ARG cc_start: 0.9234 (ttm-80) cc_final: 0.8916 (mmp-170) REVERT: T 25 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8479 (ttm110) REVERT: T 30 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7442 (ttmt) REVERT: T 201 GLN cc_start: 0.8911 (mm110) cc_final: 0.7557 (tm-30) REVERT: T 210 GLN cc_start: 0.6967 (mt0) cc_final: 0.6231 (tm-30) REVERT: U 49 ILE cc_start: 0.7509 (tp) cc_final: 0.7222 (tp) REVERT: U 79 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7736 (mmm160) REVERT: U 83 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8778 (tppt) REVERT: U 97 ARG cc_start: 0.7986 (tpt170) cc_final: 0.7338 (tpp-160) REVERT: U 104 ARG cc_start: 0.5491 (mtm180) cc_final: 0.4449 (tpm170) REVERT: U 116 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: V 62 THR cc_start: 0.8699 (p) cc_final: 0.8378 (p) REVERT: V 72 ILE cc_start: 0.6690 (pp) cc_final: 0.6445 (mm) REVERT: V 74 LYS cc_start: 0.7733 (mmtt) cc_final: 0.6653 (mtmm) REVERT: V 78 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9040 (mp) REVERT: V 119 GLN cc_start: 0.8386 (tp40) cc_final: 0.8129 (mm110) REVERT: V 168 CYS cc_start: 0.7921 (t) cc_final: 0.7592 (t) REVERT: V 179 CYS cc_start: 0.9022 (t) cc_final: 0.8764 (p) REVERT: V 185 GLU cc_start: 0.8310 (tt0) cc_final: 0.7732 (pp20) REVERT: W 72 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8722 (mp0) REVERT: W 91 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8743 (mtmm) REVERT: W 106 GLU cc_start: 0.9007 (tp30) cc_final: 0.8618 (tm-30) REVERT: W 174 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.7928 (ttp80) REVERT: W 180 LYS cc_start: 0.8425 (ttpp) cc_final: 0.7545 (mmtp) REVERT: X 50 GLU cc_start: 0.8397 (tp30) cc_final: 0.8167 (mm-30) REVERT: X 55 ASP cc_start: 0.8511 (t0) cc_final: 0.7923 (t0) REVERT: X 104 HIS cc_start: 0.9045 (OUTLIER) cc_final: 0.8677 (p-80) REVERT: X 106 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8441 (t0) REVERT: Y 35 GLU cc_start: 0.9439 (tp30) cc_final: 0.9022 (tp30) REVERT: Z 29 HIS cc_start: 0.5630 (OUTLIER) cc_final: 0.5311 (p-80) REVERT: Z 93 THR cc_start: 0.7915 (m) cc_final: 0.7579 (p) REVERT: a 4 ASP cc_start: 0.8841 (t0) cc_final: 0.8487 (p0) REVERT: a 64 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8006 (tp30) REVERT: a 82 VAL cc_start: 0.7873 (t) cc_final: 0.7620 (t) REVERT: b 24 GLN cc_start: 0.9397 (pm20) cc_final: 0.8809 (pm20) REVERT: b 88 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8014 (pttt) REVERT: b 112 ASP cc_start: 0.9348 (p0) cc_final: 0.9005 (p0) REVERT: c 140 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8786 (mmmt) REVERT: d 57 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6625 (t) REVERT: d 84 LYS cc_start: 0.9265 (ptmt) cc_final: 0.8966 (tppt) REVERT: f 22 LYS cc_start: 0.9288 (mttt) cc_final: 0.9022 (mttm) REVERT: f 26 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: g 3 LYS cc_start: 0.7547 (mtpt) cc_final: 0.6883 (mmtp) REVERT: g 35 TYR cc_start: 0.8672 (t80) cc_final: 0.8176 (t80) REVERT: h 5 ASN cc_start: 0.9119 (t0) cc_final: 0.8818 (m-40) REVERT: h 53 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7976 (tp) REVERT: h 106 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6975 (tt) REVERT: h 161 GLU cc_start: 0.8519 (tt0) cc_final: 0.8192 (tt0) REVERT: h 195 MET cc_start: 0.4750 (tmm) cc_final: 0.4452 (tmm) REVERT: h 197 LYS cc_start: 0.8232 (tptt) cc_final: 0.7946 (ttmm) REVERT: h 198 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.7401 (p) REVERT: h 234 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7324 (ttt) REVERT: h 246 ASP cc_start: 0.8694 (t0) cc_final: 0.8328 (t0) REVERT: h 287 LEU cc_start: 0.8929 (mp) cc_final: 0.8391 (tp) REVERT: h 431 ARG cc_start: 0.8338 (ttp-170) cc_final: 0.7565 (tpt170) REVERT: h 467 HIS cc_start: 0.7720 (m90) cc_final: 0.7496 (m90) REVERT: h 499 ASP cc_start: 0.8133 (p0) cc_final: 0.7709 (p0) REVERT: h 536 ASP cc_start: 0.5747 (t70) cc_final: 0.5483 (t70) REVERT: h 542 GLU cc_start: 0.7251 (tt0) cc_final: 0.6779 (tm-30) REVERT: h 580 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7085 (mmp-170) outliers start: 224 outliers final: 138 residues processed: 860 average time/residue: 0.5622 time to fit residues: 800.9334 Evaluate side-chains 796 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 644 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASN Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 189 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 226 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 10 ASN Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 116 ARG Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 121 SER Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 104 HIS Chi-restraints excluded: chain X residue 106 ASN Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 134 THR Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 122 ILE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 24 ASN Chi-restraints excluded: chain Z residue 29 HIS Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 ASN Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain c residue 18 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 26 GLN Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 31 TYR Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 41 LEU Chi-restraints excluded: chain f residue 42 ASN Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 85 HIS Chi-restraints excluded: chain h residue 90 ASN Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain h residue 114 ILE Chi-restraints excluded: chain h residue 147 PHE Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 191 LEU Chi-restraints excluded: chain h residue 198 SER Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 228 GLN Chi-restraints excluded: chain h residue 234 MET Chi-restraints excluded: chain h residue 244 MET Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 284 LEU Chi-restraints excluded: chain h residue 289 ASP Chi-restraints excluded: chain h residue 291 VAL Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 382 VAL Chi-restraints excluded: chain h residue 507 SER Chi-restraints excluded: chain h residue 509 VAL Chi-restraints excluded: chain h residue 538 VAL Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 580 ARG Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 426 optimal weight: 0.0370 chunk 451 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 404 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 101 HIS ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 180 GLN ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 116 HIS ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN b 42 GLN d 106 GLN e 72 HIS f 42 ASN h 228 GLN ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 59092 Z= 0.243 Angle : 0.715 14.202 86264 Z= 0.362 Chirality : 0.041 0.431 10796 Planarity : 0.005 0.065 6060 Dihedral : 24.129 179.419 24209 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.45 % Favored : 88.54 % Rotamer: Outliers : 5.54 % Allowed : 24.92 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 3387 helix: 0.21 (0.16), residues: 966 sheet: -2.18 (0.20), residues: 582 loop : -2.82 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 29 HIS 0.008 0.001 HIS X 92 PHE 0.028 0.002 PHE S 205 TYR 0.024 0.002 TYR h 251 ARG 0.006 0.001 ARG X 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 713 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 8 ASP cc_start: 0.8280 (m-30) cc_final: 0.8057 (m-30) REVERT: P 41 ARG cc_start: 0.7526 (ttp-170) cc_final: 0.6613 (mmt180) REVERT: P 88 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8836 (mmmm) REVERT: P 107 PHE cc_start: 0.9031 (m-80) cc_final: 0.8672 (m-80) REVERT: P 148 ASP cc_start: 0.8455 (t0) cc_final: 0.7998 (t0) REVERT: P 150 ASP cc_start: 0.8787 (p0) cc_final: 0.8384 (p0) REVERT: Q 66 VAL cc_start: 0.8484 (t) cc_final: 0.8157 (m) REVERT: Q 73 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7823 (pp) REVERT: Q 74 GLN cc_start: 0.7925 (tp40) cc_final: 0.7105 (tm-30) REVERT: Q 83 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7561 (pttt) REVERT: Q 89 ASP cc_start: 0.7608 (m-30) cc_final: 0.6992 (p0) REVERT: Q 214 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: Q 228 LEU cc_start: 0.8305 (tp) cc_final: 0.7631 (pp) REVERT: R 193 VAL cc_start: 0.9361 (t) cc_final: 0.9053 (p) REVERT: R 204 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.8978 (t) REVERT: R 230 TRP cc_start: 0.9069 (m-10) cc_final: 0.8746 (m-10) REVERT: R 238 SER cc_start: 0.7634 (OUTLIER) cc_final: 0.7221 (p) REVERT: R 244 SER cc_start: 0.8413 (t) cc_final: 0.8106 (p) REVERT: S 89 VAL cc_start: 0.9518 (t) cc_final: 0.9211 (m) REVERT: S 200 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8126 (tpp-160) REVERT: S 214 LEU cc_start: 0.9457 (mp) cc_final: 0.8908 (tp) REVERT: S 216 ASN cc_start: 0.9015 (m-40) cc_final: 0.8697 (m-40) REVERT: S 223 ASN cc_start: 0.8910 (t0) cc_final: 0.8696 (m-40) REVERT: T 20 ASP cc_start: 0.9114 (m-30) cc_final: 0.8298 (t0) REVERT: T 21 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8811 (pm20) REVERT: T 30 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7449 (tppp) REVERT: T 59 GLN cc_start: 0.9044 (mp10) cc_final: 0.8836 (mp10) REVERT: T 69 LEU cc_start: 0.7674 (mt) cc_final: 0.7042 (tp) REVERT: T 84 TYR cc_start: 0.9179 (t80) cc_final: 0.8865 (t80) REVERT: T 98 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8235 (ttm-80) REVERT: T 105 ASP cc_start: 0.8489 (t70) cc_final: 0.8124 (p0) REVERT: T 201 GLN cc_start: 0.8846 (mm110) cc_final: 0.7561 (tm-30) REVERT: T 210 GLN cc_start: 0.7053 (mt0) cc_final: 0.6399 (tm-30) REVERT: U 47 ARG cc_start: 0.7599 (ptm160) cc_final: 0.7367 (ptm160) REVERT: U 79 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7725 (mmm160) REVERT: U 83 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8788 (tppt) REVERT: U 86 GLN cc_start: 0.7659 (mt0) cc_final: 0.7386 (mm110) REVERT: U 97 ARG cc_start: 0.7992 (tpt170) cc_final: 0.7524 (tpp-160) REVERT: U 104 ARG cc_start: 0.5656 (mtm180) cc_final: 0.4613 (tpm170) REVERT: V 72 ILE cc_start: 0.6621 (pp) cc_final: 0.6416 (mm) REVERT: V 74 LYS cc_start: 0.7733 (mmtt) cc_final: 0.6758 (mtmm) REVERT: V 119 GLN cc_start: 0.8473 (tp40) cc_final: 0.8259 (mm110) REVERT: V 168 CYS cc_start: 0.7989 (t) cc_final: 0.7476 (t) REVERT: V 182 TYR cc_start: 0.8415 (p90) cc_final: 0.7613 (p90) REVERT: V 185 GLU cc_start: 0.8279 (tt0) cc_final: 0.7918 (pp20) REVERT: W 72 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8634 (mp0) REVERT: W 106 GLU cc_start: 0.8990 (tp30) cc_final: 0.8648 (tm-30) REVERT: W 175 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6656 (ttt180) REVERT: W 180 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7398 (mmtp) REVERT: X 50 GLU cc_start: 0.8287 (tp30) cc_final: 0.8040 (mm-30) REVERT: a 4 ASP cc_start: 0.8713 (t0) cc_final: 0.8358 (p0) REVERT: a 15 ARG cc_start: 0.9278 (mtm-85) cc_final: 0.9069 (mtm-85) REVERT: a 21 ASN cc_start: 0.9534 (m-40) cc_final: 0.9226 (t0) REVERT: a 49 GLU cc_start: 0.7883 (mp0) cc_final: 0.7644 (pm20) REVERT: a 64 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8009 (tp30) REVERT: a 69 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8665 (tt) REVERT: a 82 VAL cc_start: 0.7987 (t) cc_final: 0.7681 (t) REVERT: b 24 GLN cc_start: 0.9369 (pm20) cc_final: 0.8828 (pm20) REVERT: b 69 LEU cc_start: 0.8618 (tp) cc_final: 0.8355 (tp) REVERT: b 112 ASP cc_start: 0.9390 (p0) cc_final: 0.8994 (p0) REVERT: c 140 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8739 (mmmt) REVERT: d 60 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: d 74 LEU cc_start: 0.7967 (mt) cc_final: 0.7753 (mp) REVERT: d 84 LYS cc_start: 0.9211 (ptmt) cc_final: 0.8878 (tppt) REVERT: d 131 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5168 (ttp-170) REVERT: f 6 ASP cc_start: 0.8240 (t0) cc_final: 0.8006 (t0) REVERT: f 17 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7585 (ptm160) REVERT: f 22 LYS cc_start: 0.9318 (mttt) cc_final: 0.9010 (mttm) REVERT: g 20 LYS cc_start: 0.8286 (tttp) cc_final: 0.7832 (mtmm) REVERT: g 35 TYR cc_start: 0.8587 (t80) cc_final: 0.8197 (t80) REVERT: h 161 GLU cc_start: 0.8487 (tt0) cc_final: 0.8122 (tt0) REVERT: h 197 LYS cc_start: 0.8236 (tptt) cc_final: 0.7842 (ttmm) REVERT: h 229 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7522 (tpp80) REVERT: h 234 MET cc_start: 0.7447 (mtp) cc_final: 0.7076 (ttt) REVERT: h 246 ASP cc_start: 0.8633 (t0) cc_final: 0.8291 (t0) REVERT: h 287 LEU cc_start: 0.9081 (mp) cc_final: 0.8463 (tp) REVERT: h 492 ASP cc_start: 0.5718 (t0) cc_final: 0.5294 (p0) REVERT: h 499 ASP cc_start: 0.8166 (p0) cc_final: 0.7767 (p0) REVERT: h 536 ASP cc_start: 0.5806 (t70) cc_final: 0.5599 (t70) REVERT: h 542 GLU cc_start: 0.7200 (tt0) cc_final: 0.6812 (tm-30) outliers start: 160 outliers final: 110 residues processed: 803 average time/residue: 0.5498 time to fit residues: 732.3294 Evaluate side-chains 778 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 660 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 136 ARG Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 214 LYS Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 185 LYS Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 10 ASN Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 120 THR Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 106 ASN Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 18 SER Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 111 MET Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 121 ARG Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 42 ASN Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 85 HIS Chi-restraints excluded: chain h residue 90 ASN Chi-restraints excluded: chain h residue 114 ILE Chi-restraints excluded: chain h residue 121 LYS Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 227 LEU Chi-restraints excluded: chain h residue 228 GLN Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 291 VAL Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 507 SER Chi-restraints excluded: chain h residue 529 ILE Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 405 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS Q 160 HIS ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 228 GLN ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 59092 Z= 0.404 Angle : 0.850 14.342 86264 Z= 0.426 Chirality : 0.046 0.294 10796 Planarity : 0.006 0.089 6060 Dihedral : 24.283 179.463 24206 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 1.03 % Allowed : 12.55 % Favored : 86.42 % Rotamer: Outliers : 7.79 % Allowed : 25.13 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 3387 helix: -0.23 (0.16), residues: 955 sheet: -2.31 (0.20), residues: 602 loop : -2.81 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 29 HIS 0.008 0.002 HIS c 18 PHE 0.036 0.003 PHE S 205 TYR 0.030 0.003 TYR h 301 ARG 0.012 0.001 ARG d 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 677 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 8 ASP cc_start: 0.8171 (m-30) cc_final: 0.7960 (m-30) REVERT: P 34 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6484 (mt-10) REVERT: P 39 ASN cc_start: 0.8071 (m-40) cc_final: 0.7833 (t0) REVERT: P 41 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.6909 (tpp-160) REVERT: P 148 ASP cc_start: 0.8444 (t0) cc_final: 0.8038 (t0) REVERT: P 150 ASP cc_start: 0.8714 (p0) cc_final: 0.8382 (p0) REVERT: Q 45 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7299 (mppt) REVERT: Q 66 VAL cc_start: 0.8486 (t) cc_final: 0.8207 (m) REVERT: Q 74 GLN cc_start: 0.8068 (tp40) cc_final: 0.7006 (tm-30) REVERT: Q 83 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7630 (mtmt) REVERT: Q 228 LEU cc_start: 0.8278 (tp) cc_final: 0.7941 (mp) REVERT: R 193 VAL cc_start: 0.9420 (t) cc_final: 0.9093 (p) REVERT: R 204 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9025 (t) REVERT: R 230 TRP cc_start: 0.9114 (m-10) cc_final: 0.8784 (m-10) REVERT: R 238 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7031 (p) REVERT: R 244 SER cc_start: 0.8312 (t) cc_final: 0.8061 (p) REVERT: S 89 VAL cc_start: 0.9525 (t) cc_final: 0.9258 (m) REVERT: S 200 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8103 (tpp-160) REVERT: S 214 LEU cc_start: 0.9463 (mp) cc_final: 0.8855 (tp) REVERT: S 216 ASN cc_start: 0.9029 (m-40) cc_final: 0.8663 (m-40) REVERT: S 223 ASN cc_start: 0.8961 (t0) cc_final: 0.8730 (m-40) REVERT: T 21 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8795 (mm-30) REVERT: T 98 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8564 (ttm-80) REVERT: T 201 GLN cc_start: 0.8831 (mm110) cc_final: 0.7677 (tm-30) REVERT: U 44 LYS cc_start: 0.7608 (mtpt) cc_final: 0.7020 (mmmt) REVERT: U 79 ARG cc_start: 0.8382 (mmt90) cc_final: 0.7851 (mmm160) REVERT: U 83 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8932 (tppt) REVERT: U 97 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7666 (tpp-160) REVERT: U 104 ARG cc_start: 0.5661 (mtm180) cc_final: 0.5407 (mtm180) REVERT: U 116 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8123 (mtt90) REVERT: U 130 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7400 (m) REVERT: V 72 ILE cc_start: 0.7283 (pp) cc_final: 0.7066 (mm) REVERT: V 74 LYS cc_start: 0.7796 (mmtt) cc_final: 0.6888 (mtmt) REVERT: V 119 GLN cc_start: 0.8622 (tp40) cc_final: 0.8404 (mm110) REVERT: V 168 CYS cc_start: 0.7893 (t) cc_final: 0.7586 (t) REVERT: V 185 GLU cc_start: 0.8369 (tt0) cc_final: 0.7884 (pp20) REVERT: W 106 GLU cc_start: 0.9141 (tp30) cc_final: 0.8755 (tm-30) REVERT: W 180 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7548 (mmtp) REVERT: X 50 GLU cc_start: 0.8483 (tp30) cc_final: 0.8283 (pm20) REVERT: X 104 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8776 (p-80) REVERT: Y 3 ARG cc_start: 0.6647 (mmt180) cc_final: 0.6117 (mmt180) REVERT: Y 88 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.8981 (tt) REVERT: Z 29 HIS cc_start: 0.5544 (OUTLIER) cc_final: 0.5284 (p-80) REVERT: Z 93 THR cc_start: 0.7885 (m) cc_final: 0.7512 (p) REVERT: a 4 ASP cc_start: 0.8863 (t0) cc_final: 0.8542 (p0) REVERT: a 21 ASN cc_start: 0.9651 (m-40) cc_final: 0.9212 (t0) REVERT: a 49 GLU cc_start: 0.7874 (mp0) cc_final: 0.7628 (pm20) REVERT: a 64 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8443 (tp30) REVERT: a 82 VAL cc_start: 0.8216 (t) cc_final: 0.7951 (t) REVERT: b 24 GLN cc_start: 0.9399 (pm20) cc_final: 0.9114 (pm20) REVERT: b 49 GLU cc_start: 0.9151 (pp20) cc_final: 0.8914 (pp20) REVERT: b 88 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8062 (pttp) REVERT: b 112 ASP cc_start: 0.9446 (p0) cc_final: 0.9068 (p0) REVERT: c 140 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8747 (mmmt) REVERT: d 26 ASP cc_start: 0.8735 (t0) cc_final: 0.8441 (t70) REVERT: d 60 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: d 74 LEU cc_start: 0.8115 (mt) cc_final: 0.7912 (mp) REVERT: d 84 LYS cc_start: 0.9224 (ptmt) cc_final: 0.8873 (tppt) REVERT: f 18 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8828 (mtmt) REVERT: f 22 LYS cc_start: 0.9276 (mttt) cc_final: 0.8988 (mttm) REVERT: g 31 LYS cc_start: 0.7603 (mtmm) cc_final: 0.7400 (mttm) REVERT: g 35 TYR cc_start: 0.8815 (t80) cc_final: 0.8574 (t80) REVERT: h 40 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: h 105 VAL cc_start: 0.8544 (t) cc_final: 0.8147 (m) REVERT: h 106 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6509 (tt) REVERT: h 161 GLU cc_start: 0.8491 (tt0) cc_final: 0.8132 (tt0) REVERT: h 216 LYS cc_start: 0.7645 (mptt) cc_final: 0.7271 (mmtm) REVERT: h 234 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7599 (ttt) REVERT: h 246 ASP cc_start: 0.8783 (t0) cc_final: 0.8428 (t0) REVERT: h 287 LEU cc_start: 0.9160 (mp) cc_final: 0.8774 (tp) REVERT: h 374 GLU cc_start: 0.6725 (mt-10) cc_final: 0.5470 (pp20) REVERT: h 474 GLN cc_start: 0.8594 (tp40) cc_final: 0.7438 (tm-30) REVERT: h 492 ASP cc_start: 0.6563 (t0) cc_final: 0.5875 (p0) REVERT: h 499 ASP cc_start: 0.8090 (p0) cc_final: 0.7650 (p0) REVERT: h 536 ASP cc_start: 0.5995 (t70) cc_final: 0.5791 (t70) REVERT: h 542 GLU cc_start: 0.7206 (tt0) cc_final: 0.6839 (tm-30) REVERT: h 580 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7162 (mmp-170) outliers start: 225 outliers final: 155 residues processed: 810 average time/residue: 0.5579 time to fit residues: 748.6396 Evaluate side-chains 794 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 626 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASN Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 128 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 173 ILE Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 111 ARG Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 124 ASN Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 199 ASN Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 214 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 ASN Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 10 ASN Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 80 ASN Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 77 LEU Chi-restraints excluded: chain U residue 115 SER Chi-restraints excluded: chain U residue 116 ARG Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain U residue 181 ILE Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 120 THR Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 104 HIS Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 6 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 122 ILE Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Y residue 132 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 24 ASN Chi-restraints excluded: chain Z residue 29 HIS Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 120 HIS Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 132 LEU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain f residue 42 ASN Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain h residue 40 GLU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 85 HIS Chi-restraints excluded: chain h residue 90 ASN Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain h residue 114 ILE Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 191 LEU Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 219 ILE Chi-restraints excluded: chain h residue 227 LEU Chi-restraints excluded: chain h residue 234 MET Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 291 VAL Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 451 VAL Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain h residue 507 SER Chi-restraints excluded: chain h residue 509 VAL Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 580 ARG Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.0010 chunk 406 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 HIS ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 GLN e 11 ASN f 42 ASN ** h 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 HIS ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 315 ASN ** h 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 59092 Z= 0.168 Angle : 0.665 14.177 86264 Z= 0.334 Chirality : 0.038 0.348 10796 Planarity : 0.005 0.063 6060 Dihedral : 23.930 178.870 24204 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.24 % Favored : 89.75 % Rotamer: Outliers : 4.57 % Allowed : 28.63 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3387 helix: 0.35 (0.17), residues: 962 sheet: -2.04 (0.21), residues: 556 loop : -2.54 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 29 HIS 0.007 0.001 HIS R 59 PHE 0.045 0.002 PHE P 102 TYR 0.027 0.002 TYR h 251 ARG 0.015 0.001 ARG T 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 733 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 ASN cc_start: 0.8055 (m-40) cc_final: 0.7537 (t0) REVERT: P 41 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.6916 (tpp-160) REVERT: P 148 ASP cc_start: 0.8479 (t0) cc_final: 0.7908 (t70) REVERT: P 150 ASP cc_start: 0.8725 (p0) cc_final: 0.8395 (p0) REVERT: Q 66 VAL cc_start: 0.8422 (t) cc_final: 0.8163 (m) REVERT: Q 74 GLN cc_start: 0.7899 (tp40) cc_final: 0.6976 (tm-30) REVERT: Q 83 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7680 (pttt) REVERT: Q 165 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8173 (ttm110) REVERT: Q 228 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (mp) REVERT: R 190 LEU cc_start: 0.9332 (tp) cc_final: 0.9062 (tp) REVERT: R 193 VAL cc_start: 0.9325 (t) cc_final: 0.9081 (p) REVERT: R 204 THR cc_start: 0.9429 (p) cc_final: 0.8985 (t) REVERT: R 230 TRP cc_start: 0.9048 (m-10) cc_final: 0.8552 (m-10) REVERT: R 244 SER cc_start: 0.8159 (t) cc_final: 0.7896 (p) REVERT: S 89 VAL cc_start: 0.9474 (t) cc_final: 0.9171 (m) REVERT: S 200 ARG cc_start: 0.8462 (ttt180) cc_final: 0.8044 (tpp-160) REVERT: S 214 LEU cc_start: 0.9412 (mp) cc_final: 0.8706 (tp) REVERT: S 216 ASN cc_start: 0.8998 (m-40) cc_final: 0.8703 (m-40) REVERT: S 223 ASN cc_start: 0.8883 (t0) cc_final: 0.8655 (m-40) REVERT: T 20 ASP cc_start: 0.9053 (m-30) cc_final: 0.8484 (t0) REVERT: T 69 LEU cc_start: 0.7765 (mt) cc_final: 0.7148 (tp) REVERT: T 98 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7844 (ttm-80) REVERT: T 105 ASP cc_start: 0.8193 (t0) cc_final: 0.7941 (p0) REVERT: T 201 GLN cc_start: 0.8765 (mm110) cc_final: 0.7578 (tm-30) REVERT: T 210 GLN cc_start: 0.7190 (mt0) cc_final: 0.6624 (tm-30) REVERT: U 83 LYS cc_start: 0.9334 (ttmm) cc_final: 0.8782 (tppt) REVERT: U 86 GLN cc_start: 0.8458 (pp30) cc_final: 0.8110 (mm110) REVERT: U 127 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7672 (pt0) REVERT: U 130 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.7135 (m) REVERT: V 46 VAL cc_start: 0.9271 (p) cc_final: 0.8887 (m) REVERT: V 74 LYS cc_start: 0.7627 (mmtt) cc_final: 0.6652 (mtmt) REVERT: V 87 ASN cc_start: 0.8477 (t0) cc_final: 0.8026 (t0) REVERT: V 89 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7500 (mp0) REVERT: V 119 GLN cc_start: 0.8611 (tp40) cc_final: 0.8364 (mm110) REVERT: V 168 CYS cc_start: 0.7829 (t) cc_final: 0.7371 (t) REVERT: V 182 TYR cc_start: 0.8343 (p90) cc_final: 0.7653 (p90) REVERT: V 185 GLU cc_start: 0.8177 (tt0) cc_final: 0.7883 (pp20) REVERT: W 106 GLU cc_start: 0.9003 (tp30) cc_final: 0.8732 (tm-30) REVERT: W 175 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6698 (ttt180) REVERT: W 180 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7455 (mmtp) REVERT: X 104 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8688 (p-80) REVERT: X 106 ASN cc_start: 0.9060 (m-40) cc_final: 0.8836 (t0) REVERT: Y 3 ARG cc_start: 0.6447 (mmt180) cc_final: 0.6130 (mmt180) REVERT: Y 134 VAL cc_start: 0.8940 (m) cc_final: 0.8657 (t) REVERT: Z 82 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8103 (mmtm) REVERT: a 4 ASP cc_start: 0.8696 (t0) cc_final: 0.8391 (p0) REVERT: a 21 ASN cc_start: 0.9630 (m-40) cc_final: 0.9174 (t0) REVERT: a 49 GLU cc_start: 0.7981 (mp0) cc_final: 0.7701 (pm20) REVERT: a 64 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8250 (tp30) REVERT: a 69 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8714 (tt) REVERT: a 82 VAL cc_start: 0.8139 (t) cc_final: 0.7630 (t) REVERT: b 3 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7930 (mtp85) REVERT: b 24 GLN cc_start: 0.9325 (pm20) cc_final: 0.8569 (pm20) REVERT: b 69 LEU cc_start: 0.8621 (tp) cc_final: 0.8397 (tp) REVERT: b 112 ASP cc_start: 0.9342 (p0) cc_final: 0.8856 (p0) REVERT: c 120 VAL cc_start: 0.9168 (p) cc_final: 0.8941 (p) REVERT: c 137 LYS cc_start: 0.8774 (mmpt) cc_final: 0.8530 (mmpt) REVERT: c 140 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8661 (mmmt) REVERT: d 60 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: d 84 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8815 (tppt) REVERT: f 22 LYS cc_start: 0.9235 (mttt) cc_final: 0.9030 (mttm) REVERT: h 161 GLU cc_start: 0.8402 (tt0) cc_final: 0.7966 (tt0) REVERT: h 195 MET cc_start: 0.6482 (tpp) cc_final: 0.6260 (tpt) REVERT: h 246 ASP cc_start: 0.8666 (t0) cc_final: 0.8367 (t0) REVERT: h 267 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6889 (mt) REVERT: h 374 GLU cc_start: 0.6838 (mt-10) cc_final: 0.5541 (pp20) REVERT: h 474 GLN cc_start: 0.8477 (tp40) cc_final: 0.7367 (tm-30) REVERT: h 492 ASP cc_start: 0.6157 (t0) cc_final: 0.5909 (p0) REVERT: h 499 ASP cc_start: 0.8121 (p0) cc_final: 0.7722 (p0) outliers start: 132 outliers final: 79 residues processed: 811 average time/residue: 0.5487 time to fit residues: 740.1104 Evaluate side-chains 754 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 668 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 136 ARG Chi-restraints excluded: chain Q residue 157 GLN Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 17 GLU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 70 PHE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 120 THR Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 156 VAL Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain X residue 104 HIS Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 29 HIS Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 99 PHE Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 120 HIS Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 18 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 118 ILE Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 40 CYS Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 556 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 329 optimal weight: 20.0000 chunk 255 optimal weight: 0.7980 chunk 380 optimal weight: 8.9990 chunk 252 optimal weight: 0.4980 chunk 450 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN c 79 ASN d 110 GLN ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 154 ASN h 213 ASN ** h 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 59092 Z= 0.167 Angle : 0.646 14.157 86264 Z= 0.323 Chirality : 0.037 0.238 10796 Planarity : 0.005 0.060 6060 Dihedral : 23.817 179.152 24204 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.83 % Favored : 89.19 % Rotamer: Outliers : 4.43 % Allowed : 29.25 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.14), residues: 3387 helix: 0.52 (0.17), residues: 965 sheet: -1.86 (0.21), residues: 561 loop : -2.46 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 29 HIS 0.016 0.001 HIS Q 79 PHE 0.036 0.002 PHE Q 24 TYR 0.026 0.002 TYR T 84 ARG 0.007 0.000 ARG b 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 688 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 41 ARG cc_start: 0.7526 (ttp-170) cc_final: 0.6606 (mmt-90) REVERT: P 101 ARG cc_start: 0.7937 (ttt-90) cc_final: 0.7574 (ttt180) REVERT: P 148 ASP cc_start: 0.8465 (t0) cc_final: 0.7916 (t70) REVERT: P 150 ASP cc_start: 0.8777 (p0) cc_final: 0.8488 (p0) REVERT: Q 66 VAL cc_start: 0.8506 (t) cc_final: 0.8283 (m) REVERT: Q 74 GLN cc_start: 0.8034 (tp40) cc_final: 0.6967 (tm-30) REVERT: Q 83 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7696 (pttt) REVERT: Q 165 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8115 (ttm110) REVERT: Q 228 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7896 (mp) REVERT: R 116 LYS cc_start: 0.9005 (tptt) cc_final: 0.8727 (tppt) REVERT: R 193 VAL cc_start: 0.9308 (t) cc_final: 0.9042 (p) REVERT: R 204 THR cc_start: 0.9459 (p) cc_final: 0.9005 (t) REVERT: R 230 TRP cc_start: 0.8731 (m-10) cc_final: 0.8503 (m-10) REVERT: R 244 SER cc_start: 0.8065 (t) cc_final: 0.7784 (p) REVERT: S 89 VAL cc_start: 0.9437 (t) cc_final: 0.9157 (m) REVERT: S 200 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8141 (tpp-160) REVERT: S 214 LEU cc_start: 0.9280 (mp) cc_final: 0.8684 (tp) REVERT: S 216 ASN cc_start: 0.8977 (m-40) cc_final: 0.8675 (m-40) REVERT: T 23 ARG cc_start: 0.8873 (mmp-170) cc_final: 0.8012 (mmp80) REVERT: T 69 LEU cc_start: 0.7769 (mt) cc_final: 0.7149 (tp) REVERT: T 98 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7793 (ttm-80) REVERT: T 105 ASP cc_start: 0.8278 (t0) cc_final: 0.7992 (p0) REVERT: T 201 GLN cc_start: 0.8888 (mm110) cc_final: 0.7501 (tm-30) REVERT: T 210 GLN cc_start: 0.7351 (mt0) cc_final: 0.6675 (tm-30) REVERT: U 83 LYS cc_start: 0.9326 (ttmm) cc_final: 0.9079 (tptm) REVERT: U 86 GLN cc_start: 0.8436 (pp30) cc_final: 0.8086 (mm110) REVERT: U 130 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7202 (m) REVERT: V 46 VAL cc_start: 0.9266 (p) cc_final: 0.8900 (m) REVERT: V 87 ASN cc_start: 0.8513 (t0) cc_final: 0.8050 (t0) REVERT: V 89 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7509 (mp0) REVERT: V 164 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7500 (mtp180) REVERT: V 168 CYS cc_start: 0.7897 (t) cc_final: 0.7444 (t) REVERT: V 182 TYR cc_start: 0.8349 (p90) cc_final: 0.7666 (p90) REVERT: V 185 GLU cc_start: 0.8309 (tt0) cc_final: 0.8079 (pp20) REVERT: W 13 SER cc_start: 0.8449 (t) cc_final: 0.8114 (p) REVERT: W 54 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7723 (ttp-110) REVERT: W 72 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8637 (mp0) REVERT: W 106 GLU cc_start: 0.8958 (tp30) cc_final: 0.8694 (tm-30) REVERT: W 112 GLN cc_start: 0.8899 (tp40) cc_final: 0.8619 (tp40) REVERT: W 123 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.7251 (t-90) REVERT: W 175 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6736 (ttt180) REVERT: W 180 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7403 (mmtp) REVERT: Y 134 VAL cc_start: 0.8992 (m) cc_final: 0.8763 (t) REVERT: Z 82 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8144 (mmtm) REVERT: Z 121 VAL cc_start: 0.9369 (t) cc_final: 0.9071 (m) REVERT: a 4 ASP cc_start: 0.8796 (t0) cc_final: 0.8450 (p0) REVERT: a 21 ASN cc_start: 0.9632 (m-40) cc_final: 0.9184 (t0) REVERT: a 69 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8685 (tt) REVERT: a 82 VAL cc_start: 0.8223 (t) cc_final: 0.7632 (t) REVERT: b 24 GLN cc_start: 0.9236 (pm20) cc_final: 0.8504 (pm20) REVERT: b 72 CYS cc_start: 0.9196 (p) cc_final: 0.8992 (p) REVERT: b 112 ASP cc_start: 0.9325 (p0) cc_final: 0.8873 (p0) REVERT: c 137 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8595 (mmpt) REVERT: c 140 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8644 (mmmt) REVERT: d 60 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: d 84 LYS cc_start: 0.9140 (ptmt) cc_final: 0.8810 (tppt) REVERT: h 53 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7736 (tp) REVERT: h 108 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7881 (tt) REVERT: h 161 GLU cc_start: 0.8495 (tt0) cc_final: 0.8065 (tt0) REVERT: h 197 LYS cc_start: 0.8225 (tptt) cc_final: 0.7946 (ttmm) REVERT: h 216 LYS cc_start: 0.7434 (mptt) cc_final: 0.6997 (tptt) REVERT: h 226 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7973 (mp0) REVERT: h 246 ASP cc_start: 0.8641 (t0) cc_final: 0.8365 (t0) REVERT: h 267 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6806 (mt) REVERT: h 374 GLU cc_start: 0.6857 (mt-10) cc_final: 0.5500 (pp20) REVERT: h 474 GLN cc_start: 0.8521 (tp40) cc_final: 0.7423 (tm-30) REVERT: h 499 ASP cc_start: 0.7977 (p0) cc_final: 0.7652 (p0) outliers start: 128 outliers final: 86 residues processed: 754 average time/residue: 0.5457 time to fit residues: 685.3627 Evaluate side-chains 742 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 647 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 124 ASN Chi-restraints excluded: chain Q residue 157 GLN Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 189 ILE Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 189 LEU Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 120 THR Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 123 HIS Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 29 HIS Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 18 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 164 ILE Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 382 VAL Chi-restraints excluded: chain h residue 444 ASN Chi-restraints excluded: chain h residue 455 LEU Chi-restraints excluded: chain h residue 509 VAL Chi-restraints excluded: chain h residue 556 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 353 optimal weight: 0.6980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 92 HIS ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 18 HIS h 5 ASN h 90 ASN ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 59092 Z= 0.247 Angle : 0.691 14.165 86264 Z= 0.345 Chirality : 0.039 0.261 10796 Planarity : 0.005 0.063 6060 Dihedral : 23.859 179.811 24204 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.98 % Favored : 88.13 % Rotamer: Outliers : 4.67 % Allowed : 29.63 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 1.25 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3387 helix: 0.38 (0.17), residues: 972 sheet: -1.97 (0.21), residues: 583 loop : -2.52 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 29 HIS 0.008 0.001 HIS R 59 PHE 0.037 0.002 PHE Q 24 TYR 0.033 0.002 TYR R 222 ARG 0.007 0.000 ARG a 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 651 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 41 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.6732 (mmt180) REVERT: P 101 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7584 (ttt180) REVERT: P 148 ASP cc_start: 0.8405 (t0) cc_final: 0.7978 (t70) REVERT: P 150 ASP cc_start: 0.8786 (p0) cc_final: 0.8470 (p0) REVERT: Q 66 VAL cc_start: 0.8460 (t) cc_final: 0.8252 (m) REVERT: Q 74 GLN cc_start: 0.8078 (tp40) cc_final: 0.6919 (tm-30) REVERT: Q 83 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7680 (pttt) REVERT: Q 165 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8008 (ttm110) REVERT: Q 228 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8052 (mp) REVERT: R 116 LYS cc_start: 0.9020 (tptt) cc_final: 0.8763 (tppt) REVERT: R 193 VAL cc_start: 0.9328 (t) cc_final: 0.9101 (p) REVERT: R 204 THR cc_start: 0.9475 (p) cc_final: 0.9027 (t) REVERT: R 230 TRP cc_start: 0.8880 (m-10) cc_final: 0.8296 (m-10) REVERT: R 244 SER cc_start: 0.8142 (t) cc_final: 0.7869 (p) REVERT: S 89 VAL cc_start: 0.9502 (t) cc_final: 0.9208 (m) REVERT: S 200 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8238 (tpp-160) REVERT: S 214 LEU cc_start: 0.9298 (mp) cc_final: 0.8695 (tp) REVERT: S 216 ASN cc_start: 0.9029 (m-40) cc_final: 0.8699 (m-40) REVERT: T 23 ARG cc_start: 0.8918 (mmp-170) cc_final: 0.8357 (mmp80) REVERT: T 69 LEU cc_start: 0.7739 (mt) cc_final: 0.6864 (tp) REVERT: T 98 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7981 (ttm-80) REVERT: T 105 ASP cc_start: 0.8416 (t0) cc_final: 0.8119 (p0) REVERT: T 201 GLN cc_start: 0.8896 (mm110) cc_final: 0.7518 (tm-30) REVERT: U 44 LYS cc_start: 0.7424 (mtpt) cc_final: 0.6837 (mmmt) REVERT: U 83 LYS cc_start: 0.9314 (ttmm) cc_final: 0.8866 (ptmt) REVERT: U 86 GLN cc_start: 0.8515 (pp30) cc_final: 0.8152 (mm110) REVERT: U 107 ARG cc_start: 0.5011 (mtp180) cc_final: 0.4056 (mtm-85) REVERT: U 130 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7127 (m) REVERT: V 87 ASN cc_start: 0.8523 (t0) cc_final: 0.8036 (t0) REVERT: V 89 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7586 (mp0) REVERT: V 168 CYS cc_start: 0.7930 (t) cc_final: 0.7619 (t) REVERT: W 54 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7644 (mtm-85) REVERT: W 72 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8641 (mp0) REVERT: W 106 GLU cc_start: 0.8996 (tp30) cc_final: 0.8716 (tm-30) REVERT: W 112 GLN cc_start: 0.8934 (tp40) cc_final: 0.8639 (tp40) REVERT: W 123 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7345 (t-90) REVERT: W 175 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6787 (ttt180) REVERT: W 180 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7439 (mmtp) REVERT: Y 134 VAL cc_start: 0.9010 (m) cc_final: 0.8790 (t) REVERT: Z 11 SER cc_start: 0.4762 (m) cc_final: 0.4435 (p) REVERT: Z 82 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8223 (mmtm) REVERT: Z 121 VAL cc_start: 0.9408 (t) cc_final: 0.9107 (m) REVERT: a 4 ASP cc_start: 0.8779 (t0) cc_final: 0.8486 (p0) REVERT: a 21 ASN cc_start: 0.9646 (m-40) cc_final: 0.9141 (t0) REVERT: b 24 GLN cc_start: 0.9259 (pm20) cc_final: 0.8556 (pm20) REVERT: b 68 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7843 (ttt180) REVERT: b 112 ASP cc_start: 0.9355 (p0) cc_final: 0.8931 (p0) REVERT: c 137 LYS cc_start: 0.8804 (mmpt) cc_final: 0.8592 (mmpt) REVERT: c 140 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8642 (mmmt) REVERT: d 60 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: d 84 LYS cc_start: 0.9181 (ptmt) cc_final: 0.8852 (tppt) REVERT: h 53 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7767 (tp) REVERT: h 108 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7896 (tt) REVERT: h 121 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7623 (tppp) REVERT: h 161 GLU cc_start: 0.8526 (tt0) cc_final: 0.8137 (tt0) REVERT: h 197 LYS cc_start: 0.8223 (tptt) cc_final: 0.7904 (ttmm) REVERT: h 216 LYS cc_start: 0.7646 (mptt) cc_final: 0.7192 (mmtm) REVERT: h 226 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8152 (mp0) REVERT: h 234 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7688 (ttp) REVERT: h 246 ASP cc_start: 0.8664 (t0) cc_final: 0.8359 (t0) REVERT: h 267 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6732 (mt) REVERT: h 374 GLU cc_start: 0.6745 (mt-10) cc_final: 0.5659 (pp20) REVERT: h 474 GLN cc_start: 0.8625 (tp40) cc_final: 0.7590 (tm-30) REVERT: h 499 ASP cc_start: 0.7931 (p0) cc_final: 0.7605 (p0) REVERT: h 536 ASP cc_start: 0.6117 (t70) cc_final: 0.5110 (m-30) outliers start: 135 outliers final: 107 residues processed: 728 average time/residue: 0.5366 time to fit residues: 655.9278 Evaluate side-chains 743 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 627 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 128 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 124 ASN Chi-restraints excluded: chain Q residue 157 GLN Chi-restraints excluded: chain Q residue 158 SER Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 189 ILE Chi-restraints excluded: chain Q residue 199 ASN Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 117 THR Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 189 LEU Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain W residue 121 SER Chi-restraints excluded: chain W residue 123 HIS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 52 SER Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 24 ASN Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 44 ILE Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 42 ASN Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 234 MET Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 291 VAL Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 382 VAL Chi-restraints excluded: chain h residue 444 ASN Chi-restraints excluded: chain h residue 509 VAL Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 10.0000 chunk 431 optimal weight: 3.9990 chunk 393 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 329 optimal weight: 0.0270 chunk 128 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 396 optimal weight: 0.9990 chunk 417 optimal weight: 6.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 5 ASN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 59092 Z= 0.167 Angle : 0.648 14.125 86264 Z= 0.323 Chirality : 0.036 0.246 10796 Planarity : 0.005 0.064 6060 Dihedral : 23.761 178.197 24204 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.95 % Favored : 89.19 % Rotamer: Outliers : 3.91 % Allowed : 30.70 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3387 helix: 0.48 (0.17), residues: 962 sheet: -1.73 (0.21), residues: 568 loop : -2.43 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q 29 HIS 0.012 0.001 HIS P 92 PHE 0.036 0.002 PHE Q 24 TYR 0.033 0.002 TYR Q 133 ARG 0.014 0.000 ARG S 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 672 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 41 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.6788 (mmt180) REVERT: P 101 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7524 (ttt-90) REVERT: P 148 ASP cc_start: 0.8284 (t0) cc_final: 0.7972 (t70) REVERT: P 150 ASP cc_start: 0.8777 (p0) cc_final: 0.8481 (p0) REVERT: Q 74 GLN cc_start: 0.8040 (tp40) cc_final: 0.6917 (tm-30) REVERT: Q 83 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7576 (mtmt) REVERT: Q 165 ARG cc_start: 0.8548 (ttm110) cc_final: 0.8133 (ttm110) REVERT: Q 228 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7986 (mp) REVERT: R 190 LEU cc_start: 0.9104 (tp) cc_final: 0.8231 (mm) REVERT: R 193 VAL cc_start: 0.9292 (t) cc_final: 0.9083 (p) REVERT: R 204 THR cc_start: 0.9460 (p) cc_final: 0.9015 (t) REVERT: R 244 SER cc_start: 0.8125 (t) cc_final: 0.7857 (p) REVERT: S 89 VAL cc_start: 0.9473 (t) cc_final: 0.9187 (m) REVERT: S 200 ARG cc_start: 0.8534 (ttt180) cc_final: 0.8150 (tpp-160) REVERT: S 214 LEU cc_start: 0.9283 (mp) cc_final: 0.8666 (tp) REVERT: S 216 ASN cc_start: 0.8988 (m-40) cc_final: 0.8642 (m-40) REVERT: T 23 ARG cc_start: 0.9000 (mmp-170) cc_final: 0.8776 (mmp80) REVERT: T 69 LEU cc_start: 0.7770 (mt) cc_final: 0.7132 (tp) REVERT: T 98 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: T 105 ASP cc_start: 0.8367 (t0) cc_final: 0.7992 (p0) REVERT: T 201 GLN cc_start: 0.8882 (mm110) cc_final: 0.7506 (tm-30) REVERT: U 44 LYS cc_start: 0.7446 (mtpt) cc_final: 0.6946 (mmmt) REVERT: U 80 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8250 (mm-30) REVERT: U 83 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8867 (ptpt) REVERT: U 86 GLN cc_start: 0.8526 (pp30) cc_final: 0.8160 (mm110) REVERT: V 46 VAL cc_start: 0.9272 (p) cc_final: 0.8910 (m) REVERT: V 96 LEU cc_start: 0.8624 (mp) cc_final: 0.7901 (tt) REVERT: V 182 TYR cc_start: 0.8322 (p90) cc_final: 0.7815 (p90) REVERT: W 13 SER cc_start: 0.8386 (t) cc_final: 0.8073 (p) REVERT: W 54 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7723 (mtm-85) REVERT: W 72 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8638 (mp0) REVERT: W 106 GLU cc_start: 0.8932 (tp30) cc_final: 0.8696 (tm-30) REVERT: W 175 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6780 (ttt180) REVERT: W 180 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7394 (mmtp) REVERT: X 50 GLU cc_start: 0.8635 (pm20) cc_final: 0.8100 (pm20) REVERT: X 121 ASP cc_start: 0.9081 (p0) cc_final: 0.8510 (p0) REVERT: Y 35 GLU cc_start: 0.8947 (pt0) cc_final: 0.8736 (pt0) REVERT: Y 134 VAL cc_start: 0.8943 (m) cc_final: 0.8726 (t) REVERT: Z 11 SER cc_start: 0.4914 (m) cc_final: 0.4576 (p) REVERT: Z 82 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8211 (mmtm) REVERT: Z 121 VAL cc_start: 0.9378 (t) cc_final: 0.9101 (m) REVERT: a 4 ASP cc_start: 0.8756 (t0) cc_final: 0.8474 (p0) REVERT: a 21 ASN cc_start: 0.9637 (m-40) cc_final: 0.9155 (t0) REVERT: a 49 GLU cc_start: 0.7954 (pm20) cc_final: 0.7747 (pm20) REVERT: a 64 GLU cc_start: 0.8643 (tp30) cc_final: 0.8381 (tp30) REVERT: a 69 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8707 (tt) REVERT: b 3 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7658 (mtt90) REVERT: b 24 GLN cc_start: 0.9219 (pm20) cc_final: 0.8762 (pm20) REVERT: b 112 ASP cc_start: 0.9302 (p0) cc_final: 0.8901 (p0) REVERT: c 120 VAL cc_start: 0.9162 (p) cc_final: 0.8957 (p) REVERT: d 60 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: d 84 LYS cc_start: 0.9133 (ptmt) cc_final: 0.8808 (tppt) REVERT: d 98 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7763 (mm-30) REVERT: f 29 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7279 (mtm180) REVERT: h 108 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (tt) REVERT: h 121 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7653 (tppp) REVERT: h 161 GLU cc_start: 0.8520 (tt0) cc_final: 0.8187 (tt0) REVERT: h 216 LYS cc_start: 0.7450 (mptt) cc_final: 0.7060 (tptt) REVERT: h 234 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7690 (ttt) REVERT: h 246 ASP cc_start: 0.8611 (t0) cc_final: 0.8286 (t0) REVERT: h 267 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6724 (mt) REVERT: h 287 LEU cc_start: 0.9078 (mp) cc_final: 0.8579 (tp) REVERT: h 374 GLU cc_start: 0.6668 (mt-10) cc_final: 0.5562 (pp20) REVERT: h 431 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7461 (tpt90) REVERT: h 474 GLN cc_start: 0.8535 (tp40) cc_final: 0.7524 (tm-30) REVERT: h 499 ASP cc_start: 0.7774 (p0) cc_final: 0.7352 (p0) outliers start: 113 outliers final: 86 residues processed: 734 average time/residue: 0.5501 time to fit residues: 679.2324 Evaluate side-chains 735 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 642 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 124 ASN Chi-restraints excluded: chain Q residue 157 GLN Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 189 ILE Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 94 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 120 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain h residue 5 ASN Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 219 ILE Chi-restraints excluded: chain h residue 234 MET Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 382 VAL Chi-restraints excluded: chain h residue 444 ASN Chi-restraints excluded: chain h residue 451 VAL Chi-restraints excluded: chain h residue 455 LEU Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 1.9990 chunk 443 optimal weight: 20.0000 chunk 270 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 308 optimal weight: 0.5980 chunk 465 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 110 GLN h 5 ASN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.253 59092 Z= 0.294 Angle : 0.727 59.192 86264 Z= 0.376 Chirality : 0.039 0.811 10796 Planarity : 0.005 0.109 6060 Dihedral : 23.759 178.189 24204 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.10 % Favored : 89.05 % Rotamer: Outliers : 3.63 % Allowed : 31.29 % Favored : 65.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3387 helix: 0.47 (0.17), residues: 962 sheet: -1.72 (0.21), residues: 568 loop : -2.43 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.005 TRP c 136 HIS 0.039 0.001 HIS W 123 PHE 0.069 0.002 PHE U 169 TYR 0.027 0.002 TYR Q 133 ARG 0.035 0.001 ARG b 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6774 Ramachandran restraints generated. 3387 Oldfield, 0 Emsley, 3387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 641 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 41 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.6791 (mmt180) REVERT: P 101 ARG cc_start: 0.7908 (ttt-90) cc_final: 0.7527 (ttt-90) REVERT: P 148 ASP cc_start: 0.8273 (t0) cc_final: 0.7973 (t70) REVERT: P 150 ASP cc_start: 0.8778 (p0) cc_final: 0.8481 (p0) REVERT: Q 74 GLN cc_start: 0.8046 (tp40) cc_final: 0.6919 (tm-30) REVERT: Q 83 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7577 (mtmt) REVERT: Q 165 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8135 (ttm110) REVERT: Q 228 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7986 (mp) REVERT: R 190 LEU cc_start: 0.9126 (tp) cc_final: 0.8256 (mm) REVERT: R 193 VAL cc_start: 0.9297 (t) cc_final: 0.9084 (p) REVERT: R 204 THR cc_start: 0.9464 (p) cc_final: 0.9017 (t) REVERT: R 244 SER cc_start: 0.8129 (t) cc_final: 0.7860 (p) REVERT: S 89 VAL cc_start: 0.9469 (t) cc_final: 0.9188 (m) REVERT: S 200 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8146 (tpp-160) REVERT: S 214 LEU cc_start: 0.9270 (mp) cc_final: 0.8662 (tp) REVERT: S 216 ASN cc_start: 0.8971 (m-40) cc_final: 0.8640 (m-40) REVERT: T 23 ARG cc_start: 0.9001 (mmp-170) cc_final: 0.8775 (mmp80) REVERT: T 69 LEU cc_start: 0.7770 (mt) cc_final: 0.7132 (tp) REVERT: T 98 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: T 105 ASP cc_start: 0.8371 (t0) cc_final: 0.7992 (p0) REVERT: T 201 GLN cc_start: 0.8882 (mm110) cc_final: 0.7507 (tm-30) REVERT: U 44 LYS cc_start: 0.7450 (mtpt) cc_final: 0.6949 (mmmt) REVERT: U 80 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8256 (mm-30) REVERT: U 83 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8869 (ptpt) REVERT: U 86 GLN cc_start: 0.8532 (pp30) cc_final: 0.8165 (mm110) REVERT: V 46 VAL cc_start: 0.9275 (p) cc_final: 0.8912 (m) REVERT: V 96 LEU cc_start: 0.8622 (mp) cc_final: 0.7903 (tt) REVERT: V 182 TYR cc_start: 0.8323 (p90) cc_final: 0.7818 (p90) REVERT: W 13 SER cc_start: 0.8392 (t) cc_final: 0.8076 (p) REVERT: W 54 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7725 (mtm-85) REVERT: W 72 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8639 (mp0) REVERT: W 106 GLU cc_start: 0.8925 (tp30) cc_final: 0.8697 (tm-30) REVERT: W 175 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6778 (ttt180) REVERT: W 180 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7396 (mmtp) REVERT: X 50 GLU cc_start: 0.8642 (pm20) cc_final: 0.8107 (pm20) REVERT: X 121 ASP cc_start: 0.9081 (p0) cc_final: 0.8518 (p0) REVERT: Y 134 VAL cc_start: 0.8942 (m) cc_final: 0.8730 (t) REVERT: Z 11 SER cc_start: 0.4915 (m) cc_final: 0.4579 (p) REVERT: Z 82 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8215 (mmtm) REVERT: Z 121 VAL cc_start: 0.9381 (t) cc_final: 0.9101 (m) REVERT: a 4 ASP cc_start: 0.8760 (t0) cc_final: 0.8474 (p0) REVERT: a 21 ASN cc_start: 0.9622 (m-40) cc_final: 0.9143 (t0) REVERT: a 49 GLU cc_start: 0.7957 (pm20) cc_final: 0.7749 (pm20) REVERT: a 64 GLU cc_start: 0.8667 (tp30) cc_final: 0.8391 (tp30) REVERT: a 69 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8707 (tt) REVERT: b 3 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7662 (mtt90) REVERT: b 24 GLN cc_start: 0.9221 (pm20) cc_final: 0.8771 (pm20) REVERT: b 112 ASP cc_start: 0.9298 (p0) cc_final: 0.8899 (p0) REVERT: d 60 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: d 84 LYS cc_start: 0.9148 (ptmt) cc_final: 0.8810 (tppt) REVERT: d 98 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7763 (mm-30) REVERT: f 29 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7281 (mtm180) REVERT: h 53 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7673 (tp) REVERT: h 108 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7861 (tt) REVERT: h 121 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7648 (tppp) REVERT: h 161 GLU cc_start: 0.8521 (tt0) cc_final: 0.8191 (tt0) REVERT: h 216 LYS cc_start: 0.7450 (mptt) cc_final: 0.7063 (tptt) REVERT: h 234 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7682 (ttt) REVERT: h 246 ASP cc_start: 0.8611 (t0) cc_final: 0.8284 (t0) REVERT: h 267 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6682 (mt) REVERT: h 287 LEU cc_start: 0.9077 (mp) cc_final: 0.8572 (tp) REVERT: h 374 GLU cc_start: 0.6662 (mt-10) cc_final: 0.5561 (pp20) REVERT: h 431 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7455 (tpt90) REVERT: h 474 GLN cc_start: 0.8531 (tp40) cc_final: 0.7528 (tm-30) REVERT: h 499 ASP cc_start: 0.7751 (p0) cc_final: 0.7350 (p0) outliers start: 105 outliers final: 90 residues processed: 693 average time/residue: 0.5357 time to fit residues: 623.7987 Evaluate side-chains 735 residues out of total 2926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 637 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 81 PHE Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 133 ILE Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 169 SER Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain Q residue 30 PHE Chi-restraints excluded: chain Q residue 38 PHE Chi-restraints excluded: chain Q residue 105 PHE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 124 ASN Chi-restraints excluded: chain Q residue 157 GLN Chi-restraints excluded: chain Q residue 173 THR Chi-restraints excluded: chain Q residue 189 ILE Chi-restraints excluded: chain Q residue 203 ASP Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 70 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 129 VAL Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 22 HIS Chi-restraints excluded: chain T residue 98 ARG Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain V residue 27 PHE Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 152 ILE Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 80 LEU Chi-restraints excluded: chain W residue 134 ILE Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 27 ILE Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 55 ASP Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 120 HIS Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 17 LEU Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 58 PHE Chi-restraints excluded: chain d residue 60 PHE Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 86 GLU Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain e residue 8 ASN Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 108 LEU Chi-restraints excluded: chain h residue 176 ILE Chi-restraints excluded: chain h residue 184 VAL Chi-restraints excluded: chain h residue 218 ASP Chi-restraints excluded: chain h residue 219 ILE Chi-restraints excluded: chain h residue 234 MET Chi-restraints excluded: chain h residue 267 LEU Chi-restraints excluded: chain h residue 365 ASP Chi-restraints excluded: chain h residue 382 VAL Chi-restraints excluded: chain h residue 444 ASN Chi-restraints excluded: chain h residue 451 VAL Chi-restraints excluded: chain h residue 455 LEU Chi-restraints excluded: chain h residue 556 SER Chi-restraints excluded: chain h residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 0.0370 chunk 394 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 381 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 overall best weight: 3.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 5 ASN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.131822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105304 restraints weight = 125119.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.107225 restraints weight = 74253.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.107545 restraints weight = 48642.464| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.253 59092 Z= 0.294 Angle : 0.727 59.192 86264 Z= 0.376 Chirality : 0.039 0.811 10796 Planarity : 0.005 0.109 6060 Dihedral : 23.759 178.189 24204 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.10 % Favored : 89.05 % Rotamer: Outliers : 3.43 % Allowed : 31.50 % Favored : 65.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.03 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3387 helix: 0.47 (0.17), residues: 962 sheet: -1.72 (0.21), residues: 568 loop : -2.43 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.005 TRP c 136 HIS 0.039 0.001 HIS W 123 PHE 0.069 0.002 PHE U 169 TYR 0.027 0.002 TYR Q 133 ARG 0.035 0.001 ARG b 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11629.88 seconds wall clock time: 206 minutes 14.10 seconds (12374.10 seconds total)