Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:17:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2023/7ado_11732_updated.pdb" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.055 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 Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16845 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7280 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 43, 'TRANS': 871} Chain breaks: 4 Chain: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2272 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1674 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain breaks: 2 Chain: "D" Number of atoms: 509 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 64, 501 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 64, 501 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 504 Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 3 Chain: "H" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1404 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 3 Chain: "I" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1098 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'NAG': 3, 'PCW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.91, per 1000 atoms: 0.53 Number of scatterers: 16845 At special positions: 0 Unit cell: (157.472, 140.448, 177.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 5 15.00 O 3092 8.00 N 2863 7.00 C 10820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.04 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 Atom "HETATM16689 O5 NAG A1003 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 818 " " NAG A1002 " - " ASN A 370 " " NAG A1003 " - " ASN A 913 " " NAG I 301 " - " ASN I 182 " Time building additional restraints: 6.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 25 sheets defined 33.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 447 through 450 removed outlier: 3.624A pdb=" N ALA A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 481 through 501 Processing helix chain 'A' and resid 656 through 668 Proline residue: A 667 - end of helix Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 962 through 981 removed outlier: 3.759A pdb=" N SER A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 969 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 991 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 52 through 66 removed outlier: 4.143A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 82 removed outlier: 4.062A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.711A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 removed outlier: 3.626A pdb=" N ARG B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 205 through 222 removed outlier: 4.282A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.529A pdb=" N LYS B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 18 through 38 removed outlier: 4.324A pdb=" N THR C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 64 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 115 through 131 Proline residue: C 120 - end of helix removed outlier: 4.348A pdb=" N ILE C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 168 through 182 removed outlier: 5.202A pdb=" N SER C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.765A pdb=" N ALA D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 34 Processing helix chain 'E' and resid 43 through 63 removed outlier: 3.811A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 81 through 84 No H-bonds generated for 'chain 'E' and resid 81 through 84' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 96 through 99 Processing helix chain 'F' and resid 18 through 43 removed outlier: 4.020A pdb=" N CYS F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 69 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 91 through 107 removed outlier: 4.231A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'H' and resid 8 through 20 Processing helix chain 'H' and resid 68 through 85 removed outlier: 4.316A pdb=" N ASP H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 166 through 176 Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 186 through 189 No H-bonds generated for 'chain 'H' and resid 186 through 189' Processing helix chain 'H' and resid 200 through 208 Processing helix chain 'I' and resid 92 through 104 removed outlier: 3.910A pdb=" N LEU I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 140 removed outlier: 4.556A pdb=" N SER I 140 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 202 Processing helix chain 'K' and resid 2 through 15 Processing sheet with id= A, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.738A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 100 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 89 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 130 through 134 removed outlier: 5.933A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.801A pdb=" N HIS A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 191 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR A 175 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 235 through 239 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.500A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 314 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 322 through 326 Processing sheet with id= G, first strand: chain 'A' and resid 405 through 409 removed outlier: 3.567A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.840A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.614A pdb=" N THR A 588 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL A 574 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU A 572 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS A 592 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 570 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 625 through 627 removed outlier: 4.081A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 670 through 675 removed outlier: 6.412A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 723 through 725 Processing sheet with id= M, first strand: chain 'A' and resid 706 through 712 removed outlier: 7.271A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 712 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N LEU A 740 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 783 through 787 removed outlier: 4.162A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 840 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 870 through 874 removed outlier: 4.239A pdb=" N ALA A 846 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 921 through 926 Processing sheet with id= Q, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.602A pdb=" N LYS A 41 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'A' and resid 452 through 457 removed outlier: 7.345A pdb=" N VAL A 539 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 455 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 537 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 47 through 49 Processing sheet with id= T, first strand: chain 'G' and resid 93 through 96 Processing sheet with id= U, first strand: chain 'H' and resid 61 through 63 removed outlier: 4.372A pdb=" N ALA H 25 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 93 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY H 91 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA H 123 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLN H 94 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE H 125 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 29 through 31 Processing sheet with id= W, first strand: chain 'I' and resid 52 through 55 removed outlier: 3.787A pdb=" N THR I 82 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 57 through 59 Processing sheet with id= Y, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.765A pdb=" N GLN I 186 " --> pdb=" O ASP I 144 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU I 146 " --> pdb=" O GLN I 186 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLN I 188 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU I 148 " --> pdb=" O GLN I 188 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2709 1.31 - 1.44: 4686 1.44 - 1.57: 9693 1.57 - 1.69: 13 1.69 - 1.82: 110 Bond restraints: 17211 Sorted by residual: bond pdb=" C11 PCW F 201 " pdb=" O3 PCW F 201 " ideal model delta sigma weight residual 1.326 1.435 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C11 PCW C 301 " pdb=" O3 PCW C 301 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C11 PCW A1004 " pdb=" O3 PCW A1004 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C11 PCW E 201 " pdb=" O3 PCW E 201 " ideal model delta sigma weight residual 1.326 1.430 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C11 PCW A1005 " pdb=" O3 PCW A1005 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 17206 not shown) Histogram of bond angle deviations from ideal: 97.73 - 105.00: 302 105.00 - 112.27: 8603 112.27 - 119.53: 5775 119.53 - 126.80: 8375 126.80 - 134.07: 257 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N GLY A 50 " pdb=" CA GLY A 50 " pdb=" C GLY A 50 " ideal model delta sigma weight residual 113.18 102.36 10.82 2.37e+00 1.78e-01 2.08e+01 angle pdb=" N LYS G 46 " pdb=" CA LYS G 46 " pdb=" C LYS G 46 " ideal model delta sigma weight residual 108.96 115.75 -6.79 1.49e+00 4.50e-01 2.07e+01 angle pdb=" O3P PCW A1004 " pdb=" P PCW A1004 " pdb=" O4P PCW A1004 " ideal model delta sigma weight residual 96.85 110.23 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O3P PCW F 201 " pdb=" P PCW F 201 " pdb=" O4P PCW F 201 " ideal model delta sigma weight residual 96.85 109.93 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" O3P PCW A1005 " pdb=" P PCW A1005 " pdb=" O4P PCW A1005 " ideal model delta sigma weight residual 96.85 109.71 -12.86 3.00e+00 1.11e-01 1.84e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 9561 24.49 - 48.98: 597 48.98 - 73.47: 61 73.47 - 97.95: 20 97.95 - 122.44: 2 Dihedral angle restraints: 10241 sinusoidal: 4163 harmonic: 6078 Sorted by residual: dihedral pdb=" CA TYR G 136 " pdb=" C TYR G 136 " pdb=" N PRO G 137 " pdb=" CA PRO G 137 " ideal model delta harmonic sigma weight residual -180.00 -128.26 -51.74 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASP A 427 " pdb=" C ASP A 427 " pdb=" N HIS A 428 " pdb=" CA HIS A 428 " ideal model delta harmonic sigma weight residual 180.00 129.04 50.96 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLU A 232 " pdb=" C GLU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 132.44 47.56 0 5.00e+00 4.00e-02 9.05e+01 ... (remaining 10238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2578 0.125 - 0.250: 46 0.250 - 0.374: 0 0.374 - 0.499: 0 0.499 - 0.624: 1 Chirality restraints: 2625 Sorted by residual: chirality pdb=" C1 NAG I 301 " pdb=" ND2 ASN I 182 " pdb=" C2 NAG I 301 " pdb=" O5 NAG I 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" CA PRO A 883 " pdb=" N PRO A 883 " pdb=" C PRO A 883 " pdb=" CB PRO A 883 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PCW F 201 " pdb=" C1 PCW F 201 " pdb=" C3 PCW F 201 " pdb=" O2 PCW F 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2622 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 913 " 0.005 2.00e-02 2.50e+03 2.67e-01 8.92e+02 pdb=" CG ASN A 913 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 913 " -0.206 2.00e-02 2.50e+03 pdb=" ND2 ASN A 913 " 0.463 2.00e-02 2.50e+03 pdb=" C1 NAG A1003 " -0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 182 " -0.192 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" CG ASN I 182 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN I 182 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN I 182 " 0.447 2.00e-02 2.50e+03 pdb=" C1 NAG I 301 " -0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 370 " 0.159 2.00e-02 2.50e+03 1.94e-01 4.72e+02 pdb=" CG ASN A 370 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 370 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 370 " -0.323 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " 0.238 2.00e-02 2.50e+03 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 109 2.49 - 3.09: 13002 3.09 - 3.70: 24643 3.70 - 4.30: 33872 4.30 - 4.90: 57953 Nonbonded interactions: 129579 Sorted by model distance: nonbonded pdb=" O GLN A 533 " pdb=" OG SER A 550 " model vdw 1.890 2.440 nonbonded pdb=" OD1 ASP A 459 " pdb=" OG1 THR A 578 " model vdw 2.003 2.440 nonbonded pdb=" O LEU H 174 " pdb=" OG SER H 177 " model vdw 2.105 2.440 nonbonded pdb=" OG SER I 136 " pdb=" O GLY I 166 " model vdw 2.120 2.440 nonbonded pdb=" O ASP C 85 " pdb=" NZ LYS C 90 " model vdw 2.139 2.520 ... (remaining 129574 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 65 5.16 5 C 10820 2.51 5 N 2863 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.010 Extract box with map and model: 14.520 Check model and map are aligned: 0.240 Process input model: 42.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.008 0.109 17211 Z= 0.518 Angle : 0.958 13.384 23312 Z= 0.494 Chirality : 0.049 0.624 2625 Planarity : 0.008 0.116 2934 Dihedral : 15.826 122.442 6304 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 3.53 % Twisted General : 0.41 % 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: -4.86 (0.14), residues: 2020 helix: -2.40 (0.16), residues: 679 sheet: -2.32 (0.22), residues: 408 loop : -4.36 (0.14), residues: 933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.3407 time to fit residues: 115.2923 Evaluate side-chains 160 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 376 ASN A 533 GLN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 185 ASN C 231 GLN H 142 HIS H 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17211 Z= 0.226 Angle : 0.696 12.210 23312 Z= 0.365 Chirality : 0.045 0.274 2625 Planarity : 0.005 0.086 2934 Dihedral : 9.039 105.494 2348 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.76 % Favored : 90.19 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.17), residues: 2020 helix: -0.51 (0.19), residues: 680 sheet: -1.32 (0.24), residues: 419 loop : -3.65 (0.16), residues: 921 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.3163 time to fit residues: 95.1919 Evaluate side-chains 169 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1509 time to fit residues: 6.2131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN H 203 ASN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17211 Z= 0.214 Angle : 0.653 11.755 23312 Z= 0.340 Chirality : 0.044 0.175 2625 Planarity : 0.004 0.083 2934 Dihedral : 8.434 104.886 2348 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 2020 helix: 0.26 (0.20), residues: 689 sheet: -0.79 (0.25), residues: 424 loop : -3.45 (0.16), residues: 907 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 198 average time/residue: 0.3036 time to fit residues: 91.8837 Evaluate side-chains 168 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1516 time to fit residues: 6.1035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 186 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17211 Z= 0.204 Angle : 0.623 11.465 23312 Z= 0.324 Chirality : 0.043 0.185 2625 Planarity : 0.004 0.082 2934 Dihedral : 7.876 104.082 2348 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2020 helix: 0.63 (0.20), residues: 688 sheet: -0.45 (0.25), residues: 429 loop : -3.28 (0.17), residues: 903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 184 average time/residue: 0.2945 time to fit residues: 82.8259 Evaluate side-chains 168 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1587 time to fit residues: 6.1864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS H 106 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.082 17211 Z= 0.497 Angle : 0.774 10.816 23312 Z= 0.400 Chirality : 0.048 0.230 2625 Planarity : 0.005 0.083 2934 Dihedral : 8.056 105.140 2348 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2020 helix: 0.30 (0.20), residues: 695 sheet: -0.72 (0.25), residues: 448 loop : -3.27 (0.18), residues: 877 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 197 average time/residue: 0.3145 time to fit residues: 92.5037 Evaluate side-chains 173 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1631 time to fit residues: 7.5474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17211 Z= 0.261 Angle : 0.652 11.328 23312 Z= 0.340 Chirality : 0.044 0.167 2625 Planarity : 0.005 0.080 2934 Dihedral : 7.700 104.139 2348 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 2020 helix: 0.62 (0.20), residues: 697 sheet: -0.53 (0.25), residues: 442 loop : -3.16 (0.18), residues: 881 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 188 average time/residue: 0.3102 time to fit residues: 87.7474 Evaluate side-chains 180 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1553 time to fit residues: 7.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 152 GLN H 106 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17211 Z= 0.208 Angle : 0.637 10.965 23312 Z= 0.330 Chirality : 0.043 0.168 2625 Planarity : 0.004 0.082 2934 Dihedral : 7.434 100.585 2348 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 2020 helix: 0.85 (0.21), residues: 693 sheet: -0.37 (0.25), residues: 453 loop : -3.07 (0.18), residues: 874 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 186 average time/residue: 0.3188 time to fit residues: 88.3803 Evaluate side-chains 167 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1501 time to fit residues: 3.5825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17211 Z= 0.174 Angle : 0.625 10.631 23312 Z= 0.322 Chirality : 0.042 0.170 2625 Planarity : 0.004 0.082 2934 Dihedral : 7.092 96.045 2348 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 2020 helix: 0.99 (0.21), residues: 697 sheet: -0.16 (0.25), residues: 441 loop : -2.95 (0.18), residues: 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 189 average time/residue: 0.3168 time to fit residues: 89.3821 Evaluate side-chains 173 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1625 time to fit residues: 5.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0970 chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN G 87 HIS ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 17211 Z= 0.209 Angle : 0.649 10.664 23312 Z= 0.330 Chirality : 0.043 0.209 2625 Planarity : 0.004 0.080 2934 Dihedral : 7.020 93.029 2348 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 2020 helix: 0.97 (0.21), residues: 698 sheet: -0.11 (0.25), residues: 449 loop : -2.94 (0.18), residues: 873 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 173 average time/residue: 0.3263 time to fit residues: 84.0927 Evaluate side-chains 167 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1614 time to fit residues: 3.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 50.0000 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.0370 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS D 152 GLN E 87 HIS ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 17211 Z= 0.219 Angle : 0.650 10.255 23312 Z= 0.332 Chirality : 0.043 0.194 2625 Planarity : 0.004 0.079 2934 Dihedral : 6.886 89.638 2348 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 2020 helix: 1.04 (0.21), residues: 691 sheet: -0.09 (0.25), residues: 449 loop : -2.90 (0.18), residues: 880 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 168 average time/residue: 0.3127 time to fit residues: 79.3365 Evaluate side-chains 165 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1574 time to fit residues: 3.4000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.098750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067810 restraints weight = 43818.968| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.73 r_work: 0.2924 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17211 Z= 0.212 Angle : 0.650 10.265 23312 Z= 0.332 Chirality : 0.043 0.204 2625 Planarity : 0.004 0.076 2934 Dihedral : 6.787 86.653 2348 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 2020 helix: 1.03 (0.21), residues: 697 sheet: -0.07 (0.25), residues: 449 loop : -2.85 (0.19), residues: 874 =============================================================================== Job complete usr+sys time: 3459.11 seconds wall clock time: 63 minutes 30.98 seconds (3810.98 seconds total)