Starting phenix.real_space_refine on Fri Feb 16 23:32:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2024/7ado_11732_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2024/7ado_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_2024/7ado_11732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2024/7ado_11732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2024/7ado_11732_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ado_11732/02_2024/7ado_11732_updated.pdb" } resolution = 3.39 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= 0.055 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 66 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: 31 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.43, per 1000 atoms: 0.56 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: 6.69 Conformation dependent library (CDL) restraints added in 3.1 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: 3.59 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: 5.61 Time building geometry restraints manager: 7.19 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: 9631 24.49 - 48.98: 620 48.98 - 73.47: 68 73.47 - 97.95: 22 97.95 - 122.44: 2 Dihedral angle restraints: 10343 sinusoidal: 4265 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 10340 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 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: 3.430 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: 0.020 Extract box with map and model: 13.910 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.720 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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= 0.520 Angle : 0.962 13.384 23312 Z= 0.494 Chirality : 0.049 0.624 2625 Planarity : 0.008 0.116 2934 Dihedral : 16.076 122.442 6406 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 % Allowed : 4.26 % Favored : 95.63 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 696 HIS 0.007 0.001 HIS A 160 PHE 0.031 0.002 PHE G 84 TYR 0.022 0.002 TYR A 938 ARG 0.027 0.003 ARG I 111 *********************** 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 : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7495 (pp20) cc_final: 0.7114 (pp20) REVERT: B 25 GLU cc_start: 0.7845 (pp20) cc_final: 0.7611 (pp20) REVERT: B 163 GLU cc_start: 0.7267 (tt0) cc_final: 0.6893 (tm-30) REVERT: C 59 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8852 (mtp-110) REVERT: C 63 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 154 MET cc_start: 0.6963 (mmp) cc_final: 0.6523 (ptt) REVERT: E 70 MET cc_start: 0.8674 (ptt) cc_final: 0.8443 (ptt) REVERT: E 71 ASP cc_start: 0.8507 (t70) cc_final: 0.8007 (t0) REVERT: F 86 THR cc_start: 0.8780 (m) cc_final: 0.8477 (p) REVERT: G 45 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.4064 (m-80) REVERT: H 5 LYS cc_start: 0.7227 (mptt) cc_final: 0.6101 (tttp) REVERT: H 96 ASN cc_start: 0.8140 (m-40) cc_final: 0.7794 (t0) REVERT: H 109 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8526 (mt-10) REVERT: H 142 HIS cc_start: 0.7494 (t-90) cc_final: 0.6890 (t70) REVERT: H 181 GLU cc_start: 0.8011 (mp0) cc_final: 0.7630 (mp0) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.3438 time to fit residues: 115.5573 Evaluate side-chains 165 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 PHE 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: 5.9990 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 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN C 231 GLN H 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1595 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= 0.222 Angle : 0.703 12.170 23312 Z= 0.366 Chirality : 0.045 0.210 2625 Planarity : 0.005 0.084 2934 Dihedral : 10.159 104.223 2452 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.51 % Favored : 90.44 % Rotamer: Outliers : 1.11 % Allowed : 10.90 % Favored : 87.99 % 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: -3.11 (0.17), residues: 2020 helix: -0.56 (0.19), residues: 673 sheet: -1.36 (0.24), residues: 421 loop : -3.66 (0.16), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 796 HIS 0.004 0.001 HIS H 147 PHE 0.016 0.001 PHE C 132 TYR 0.019 0.001 TYR H 93 ARG 0.006 0.001 ARG I 169 *********************** 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 205 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8533 (m-30) cc_final: 0.8318 (m-30) REVERT: A 759 ILE cc_start: 0.8459 (mm) cc_final: 0.8238 (tt) REVERT: B 185 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8331 (p0) REVERT: C 59 ARG cc_start: 0.9121 (mtp-110) cc_final: 0.8687 (mtp-110) REVERT: C 92 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7535 (mmtm) REVERT: C 236 ASP cc_start: 0.8765 (t0) cc_final: 0.8564 (t0) REVERT: E 70 MET cc_start: 0.8656 (ptt) cc_final: 0.8040 (ptt) REVERT: E 71 ASP cc_start: 0.8280 (t70) cc_final: 0.8054 (t0) REVERT: H 5 LYS cc_start: 0.7457 (mptt) cc_final: 0.6162 (tttp) REVERT: H 96 ASN cc_start: 0.8080 (m-40) cc_final: 0.7744 (t0) REVERT: H 109 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8594 (mt-10) REVERT: H 142 HIS cc_start: 0.7034 (t-90) cc_final: 0.6040 (t70) REVERT: H 144 TYR cc_start: 0.8563 (m-80) cc_final: 0.8354 (m-80) REVERT: H 181 GLU cc_start: 0.8118 (mp0) cc_final: 0.7905 (mp0) REVERT: H 188 ASN cc_start: 0.9126 (m-40) cc_final: 0.8778 (m-40) outliers start: 20 outliers final: 14 residues processed: 198 average time/residue: 0.3034 time to fit residues: 90.0867 Evaluate side-chains 171 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain H residue 12 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.0070 chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 533 GLN B 155 GLN B 169 HIS B 185 ASN B 263 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN H 106 GLN H 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17211 Z= 0.176 Angle : 0.645 11.929 23312 Z= 0.334 Chirality : 0.043 0.174 2625 Planarity : 0.004 0.083 2934 Dihedral : 9.452 104.755 2450 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.44 % Allowed : 13.78 % Favored : 84.78 % 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: -2.28 (0.18), residues: 2020 helix: 0.29 (0.20), residues: 688 sheet: -0.81 (0.25), residues: 422 loop : -3.42 (0.16), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 796 HIS 0.004 0.001 HIS H 147 PHE 0.017 0.001 PHE A 128 TYR 0.016 0.001 TYR H 93 ARG 0.008 0.000 ARG H 169 *********************** 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 210 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.944 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: A 177 MET cc_start: 0.6953 (mtp) cc_final: 0.6448 (mtm) REVERT: A 426 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: A 429 LEU cc_start: 0.7645 (tp) cc_final: 0.7381 (tp) REVERT: B 19 MET cc_start: 0.7743 (mmm) cc_final: 0.7521 (ttm) REVERT: C 92 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7489 (mmtm) REVERT: C 236 ASP cc_start: 0.8709 (t0) cc_final: 0.8405 (t0) REVERT: D 154 MET cc_start: 0.7099 (mmp) cc_final: 0.6448 (ptt) REVERT: E 70 MET cc_start: 0.8727 (ptt) cc_final: 0.8175 (ptt) REVERT: H 5 LYS cc_start: 0.7538 (mptt) cc_final: 0.6166 (tttp) REVERT: H 14 MET cc_start: 0.7954 (tpp) cc_final: 0.7688 (tpp) REVERT: H 96 ASN cc_start: 0.8124 (m-40) cc_final: 0.7696 (t0) REVERT: H 109 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8605 (mt-10) REVERT: H 110 LYS cc_start: 0.7698 (mmmm) cc_final: 0.7485 (mmtt) REVERT: H 142 HIS cc_start: 0.6786 (t-90) cc_final: 0.5537 (t-90) REVERT: H 144 TYR cc_start: 0.8320 (m-80) cc_final: 0.7979 (m-80) REVERT: H 188 ASN cc_start: 0.9165 (m-40) cc_final: 0.8760 (m110) outliers start: 26 outliers final: 15 residues processed: 202 average time/residue: 0.3139 time to fit residues: 94.8973 Evaluate side-chains 172 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain H residue 106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.1980 chunk 139 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 263 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN H 188 ASN H 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17211 Z= 0.322 Angle : 0.679 11.316 23312 Z= 0.351 Chirality : 0.045 0.179 2625 Planarity : 0.005 0.083 2934 Dihedral : 8.948 105.767 2450 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.60 % Allowed : 14.78 % Favored : 82.62 % 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: -2.01 (0.18), residues: 2020 helix: 0.44 (0.20), residues: 691 sheet: -0.63 (0.25), residues: 446 loop : -3.29 (0.17), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 61 HIS 0.004 0.001 HIS A 428 PHE 0.021 0.002 PHE A 128 TYR 0.016 0.001 TYR A 898 ARG 0.004 0.000 ARG H 169 *********************** 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 224 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7041 (mtp) cc_final: 0.6585 (mtm) REVERT: C 92 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7622 (mmtm) REVERT: C 236 ASP cc_start: 0.8852 (t0) cc_final: 0.8576 (t0) REVERT: D 17 TRP cc_start: 0.8760 (m100) cc_final: 0.8386 (m100) REVERT: D 51 GLN cc_start: 0.8952 (mm110) cc_final: 0.8664 (mm-40) REVERT: D 154 MET cc_start: 0.6963 (mmp) cc_final: 0.6449 (ptt) REVERT: D 172 GLU cc_start: 0.8590 (pp20) cc_final: 0.8030 (pp20) REVERT: E 70 MET cc_start: 0.8778 (ptt) cc_final: 0.8219 (ptt) REVERT: H 5 LYS cc_start: 0.7589 (mptt) cc_final: 0.6227 (tttp) REVERT: H 14 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7712 (tpp) REVERT: H 96 ASN cc_start: 0.8401 (m-40) cc_final: 0.7884 (t0) REVERT: H 109 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8711 (mt-10) REVERT: H 110 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7674 (mmtp) REVERT: H 142 HIS cc_start: 0.6625 (t-90) cc_final: 0.5358 (t-90) REVERT: H 144 TYR cc_start: 0.8381 (m-80) cc_final: 0.8138 (m-80) REVERT: H 178 ARG cc_start: 0.8371 (tmm160) cc_final: 0.8054 (tpt90) REVERT: H 181 GLU cc_start: 0.8175 (mp0) cc_final: 0.7445 (mp0) REVERT: H 188 ASN cc_start: 0.9224 (m110) cc_final: 0.8829 (m-40) outliers start: 47 outliers final: 26 residues processed: 205 average time/residue: 0.2977 time to fit residues: 91.8818 Evaluate side-chains 184 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 129 ASN C 247 HIS H 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17211 Z= 0.382 Angle : 0.699 11.298 23312 Z= 0.361 Chirality : 0.046 0.181 2625 Planarity : 0.005 0.081 2934 Dihedral : 8.893 105.152 2450 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.07 % 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: -1.92 (0.18), residues: 2020 helix: 0.53 (0.20), residues: 694 sheet: -0.57 (0.25), residues: 442 loop : -3.26 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 61 HIS 0.004 0.001 HIS H 147 PHE 0.024 0.002 PHE A 128 TYR 0.017 0.001 TYR A 898 ARG 0.010 0.001 ARG F 20 *********************** 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 231 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7070 (mtp) cc_final: 0.6720 (mtp) REVERT: B 19 MET cc_start: 0.7951 (mmm) cc_final: 0.7680 (ttm) REVERT: B 226 MET cc_start: 0.8725 (mmm) cc_final: 0.8502 (mmm) REVERT: C 92 LYS cc_start: 0.8251 (mmtt) cc_final: 0.8023 (mmtm) REVERT: C 236 ASP cc_start: 0.8931 (t0) cc_final: 0.8615 (t0) REVERT: D 17 TRP cc_start: 0.8877 (m100) cc_final: 0.8621 (m100) REVERT: D 154 MET cc_start: 0.6984 (mmp) cc_final: 0.6503 (ptt) REVERT: D 157 LEU cc_start: 0.6377 (tp) cc_final: 0.5642 (pp) REVERT: D 172 GLU cc_start: 0.8599 (pp20) cc_final: 0.7972 (pp20) REVERT: E 70 MET cc_start: 0.8812 (ptt) cc_final: 0.8505 (ptt) REVERT: H 5 LYS cc_start: 0.7680 (mptt) cc_final: 0.6316 (tttp) REVERT: H 14 MET cc_start: 0.7903 (tpp) cc_final: 0.7648 (tpp) REVERT: H 96 ASN cc_start: 0.8487 (m-40) cc_final: 0.7993 (t0) REVERT: H 109 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8678 (mt-10) REVERT: H 142 HIS cc_start: 0.6630 (t-90) cc_final: 0.5505 (t-90) REVERT: H 181 GLU cc_start: 0.8189 (mp0) cc_final: 0.7094 (mp0) REVERT: H 188 ASN cc_start: 0.9242 (m110) cc_final: 0.8862 (m-40) outliers start: 56 outliers final: 36 residues processed: 213 average time/residue: 0.2939 time to fit residues: 93.9154 Evaluate side-chains 204 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 168 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.5732 ------------------------------------------------------------------------------- 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 860 HIS C 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17211 Z= 0.165 Angle : 0.614 11.389 23312 Z= 0.316 Chirality : 0.042 0.170 2625 Planarity : 0.004 0.076 2934 Dihedral : 8.371 103.844 2450 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 2.05 % Allowed : 17.71 % Favored : 80.24 % 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: -1.52 (0.19), residues: 2020 helix: 0.88 (0.21), residues: 697 sheet: -0.35 (0.25), residues: 438 loop : -3.04 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 119 HIS 0.004 0.001 HIS H 147 PHE 0.020 0.001 PHE A 128 TYR 0.015 0.001 TYR H 144 ARG 0.012 0.001 ARG H 178 *********************** 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 220 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7996 (t70) cc_final: 0.7522 (t0) REVERT: A 675 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6822 (p0) REVERT: B 24 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8131 (mp0) REVERT: B 25 GLU cc_start: 0.8638 (pp20) cc_final: 0.8135 (pp20) REVERT: B 226 MET cc_start: 0.8713 (mmm) cc_final: 0.8484 (mmm) REVERT: C 92 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7928 (mmtm) REVERT: C 236 ASP cc_start: 0.8838 (t0) cc_final: 0.8572 (t0) REVERT: D 17 TRP cc_start: 0.8827 (m100) cc_final: 0.8549 (m100) REVERT: D 154 MET cc_start: 0.6995 (mmp) cc_final: 0.6568 (ptt) REVERT: D 157 LEU cc_start: 0.6206 (tp) cc_final: 0.5582 (pp) REVERT: D 172 GLU cc_start: 0.8581 (pp20) cc_final: 0.8011 (pp20) REVERT: E 70 MET cc_start: 0.8732 (ptt) cc_final: 0.8438 (ptt) REVERT: G 136 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.4961 (t80) REVERT: H 5 LYS cc_start: 0.7675 (mptt) cc_final: 0.6321 (tttp) REVERT: H 14 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (tpp) REVERT: H 96 ASN cc_start: 0.8448 (m-40) cc_final: 0.7960 (t0) REVERT: H 109 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8628 (mt-10) REVERT: H 142 HIS cc_start: 0.6683 (t-90) cc_final: 0.5568 (t-90) REVERT: H 188 ASN cc_start: 0.9282 (m110) cc_final: 0.8900 (m-40) outliers start: 37 outliers final: 24 residues processed: 206 average time/residue: 0.3027 time to fit residues: 93.3182 Evaluate side-chains 197 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 161 VAL 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: 8.9990 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17211 Z= 0.333 Angle : 0.665 10.781 23312 Z= 0.343 Chirality : 0.045 0.181 2625 Planarity : 0.005 0.078 2934 Dihedral : 8.415 102.661 2450 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.49 % Allowed : 18.54 % Favored : 78.97 % 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: -1.56 (0.19), residues: 2020 helix: 0.87 (0.21), residues: 694 sheet: -0.42 (0.25), residues: 453 loop : -3.10 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 61 HIS 0.004 0.001 HIS A 860 PHE 0.022 0.001 PHE A 128 TYR 0.014 0.001 TYR A 938 ARG 0.012 0.000 ARG F 20 *********************** 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 218 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7150 (ttm) cc_final: 0.6814 (mtp) REVERT: A 231 ASP cc_start: 0.8103 (t70) cc_final: 0.7710 (t0) REVERT: B 19 MET cc_start: 0.8021 (mmm) cc_final: 0.7725 (ttm) REVERT: B 25 GLU cc_start: 0.8627 (pp20) cc_final: 0.8070 (pp20) REVERT: C 93 ARG cc_start: 0.7464 (mmm160) cc_final: 0.7062 (mmm160) REVERT: C 236 ASP cc_start: 0.8947 (t0) cc_final: 0.8680 (t0) REVERT: D 17 TRP cc_start: 0.8888 (m100) cc_final: 0.8609 (m100) REVERT: D 154 MET cc_start: 0.6924 (mmp) cc_final: 0.6523 (ptt) REVERT: D 157 LEU cc_start: 0.6227 (tp) cc_final: 0.5618 (pp) REVERT: D 172 GLU cc_start: 0.8633 (pp20) cc_final: 0.8014 (pp20) REVERT: E 70 MET cc_start: 0.8787 (ptt) cc_final: 0.8526 (ptt) REVERT: G 136 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4997 (t80) REVERT: H 5 LYS cc_start: 0.7677 (mptt) cc_final: 0.6312 (tttp) REVERT: H 14 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7655 (tpt) REVERT: H 109 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8677 (mt-10) REVERT: H 142 HIS cc_start: 0.6682 (t-90) cc_final: 0.5655 (t-90) REVERT: H 188 ASN cc_start: 0.9254 (m110) cc_final: 0.8918 (m-40) outliers start: 45 outliers final: 34 residues processed: 202 average time/residue: 0.2904 time to fit residues: 88.5772 Evaluate side-chains 204 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 783 HIS G 87 HIS H 106 GLN H 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17211 Z= 0.221 Angle : 0.628 10.984 23312 Z= 0.323 Chirality : 0.043 0.188 2625 Planarity : 0.004 0.076 2934 Dihedral : 8.220 101.202 2450 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.21 % Allowed : 19.15 % Favored : 78.64 % 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: -1.44 (0.19), residues: 2020 helix: 0.86 (0.20), residues: 706 sheet: -0.31 (0.25), residues: 452 loop : -3.00 (0.18), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 61 HIS 0.005 0.001 HIS A 783 PHE 0.021 0.001 PHE A 128 TYR 0.016 0.001 TYR H 180 ARG 0.008 0.000 ARG C 59 *********************** 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 220 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7133 (ttm) cc_final: 0.6782 (mtp) REVERT: A 231 ASP cc_start: 0.8010 (t70) cc_final: 0.7564 (t0) REVERT: B 24 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8095 (mp0) REVERT: B 25 GLU cc_start: 0.8669 (pp20) cc_final: 0.8164 (pp20) REVERT: B 226 MET cc_start: 0.8777 (mmm) cc_final: 0.8553 (mmm) REVERT: C 93 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7093 (mmm160) REVERT: C 236 ASP cc_start: 0.8920 (t0) cc_final: 0.8690 (t0) REVERT: D 17 TRP cc_start: 0.8864 (m100) cc_final: 0.8646 (m100) REVERT: D 154 MET cc_start: 0.6952 (mmp) cc_final: 0.6588 (ptt) REVERT: D 157 LEU cc_start: 0.6074 (tp) cc_final: 0.5530 (pp) REVERT: D 172 GLU cc_start: 0.8621 (pp20) cc_final: 0.8024 (pp20) REVERT: E 70 MET cc_start: 0.8735 (ptt) cc_final: 0.8496 (ptt) REVERT: G 136 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.5053 (t80) REVERT: H 5 LYS cc_start: 0.7671 (mptt) cc_final: 0.6271 (tttp) REVERT: H 14 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7585 (tpp) REVERT: H 109 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8571 (mm-30) REVERT: H 142 HIS cc_start: 0.6551 (t-90) cc_final: 0.5484 (t-90) REVERT: H 188 ASN cc_start: 0.9251 (m-40) cc_final: 0.8932 (m-40) outliers start: 40 outliers final: 33 residues processed: 206 average time/residue: 0.3116 time to fit residues: 95.8368 Evaluate side-chains 206 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0570 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17211 Z= 0.280 Angle : 0.658 10.639 23312 Z= 0.338 Chirality : 0.044 0.204 2625 Planarity : 0.004 0.075 2934 Dihedral : 8.193 99.742 2450 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 2.27 % Allowed : 19.15 % Favored : 78.58 % 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: -1.44 (0.19), residues: 2020 helix: 0.86 (0.20), residues: 705 sheet: -0.30 (0.25), residues: 449 loop : -2.99 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 17 HIS 0.003 0.001 HIS A 860 PHE 0.022 0.001 PHE A 128 TYR 0.014 0.001 TYR E 58 ARG 0.009 0.000 ARG C 59 *********************** 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 216 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7132 (ttm) cc_final: 0.6542 (mtm) REVERT: A 231 ASP cc_start: 0.8043 (t70) cc_final: 0.7624 (t0) REVERT: B 24 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8092 (mp0) REVERT: B 25 GLU cc_start: 0.8667 (pp20) cc_final: 0.8135 (pp20) REVERT: B 226 MET cc_start: 0.8784 (mmm) cc_final: 0.8570 (mmm) REVERT: C 236 ASP cc_start: 0.8964 (t0) cc_final: 0.8732 (t0) REVERT: D 51 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8417 (mm110) REVERT: D 154 MET cc_start: 0.6928 (mmp) cc_final: 0.6587 (ptt) REVERT: D 172 GLU cc_start: 0.8635 (pp20) cc_final: 0.8013 (pp20) REVERT: E 70 MET cc_start: 0.8768 (ptt) cc_final: 0.8555 (ptt) REVERT: G 136 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.5124 (t80) REVERT: H 5 LYS cc_start: 0.7682 (mptt) cc_final: 0.6264 (tttp) REVERT: H 14 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7642 (tpt) REVERT: H 109 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8629 (mm-30) REVERT: H 142 HIS cc_start: 0.6601 (t-90) cc_final: 0.5623 (t-90) REVERT: H 181 GLU cc_start: 0.8474 (mp0) cc_final: 0.8041 (mp0) REVERT: H 188 ASN cc_start: 0.9218 (m-40) cc_final: 0.8894 (m-40) outliers start: 41 outliers final: 36 residues processed: 201 average time/residue: 0.2970 time to fit residues: 89.7060 Evaluate side-chains 207 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 14 MET Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL 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: 4.9990 chunk 91 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 50.0000 chunk 187 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17211 Z= 0.313 Angle : 0.685 10.666 23312 Z= 0.351 Chirality : 0.045 0.178 2625 Planarity : 0.005 0.074 2934 Dihedral : 8.210 97.076 2450 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.43 % Allowed : 19.42 % Favored : 78.14 % 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: -1.45 (0.19), residues: 2020 helix: 0.92 (0.20), residues: 700 sheet: -0.36 (0.25), residues: 452 loop : -3.01 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 61 HIS 0.004 0.001 HIS A 860 PHE 0.021 0.001 PHE A 128 TYR 0.012 0.001 TYR A 938 ARG 0.011 0.000 ARG H 152 ********************** 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 217 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7111 (ttm) cc_final: 0.6779 (mtp) REVERT: A 231 ASP cc_start: 0.8048 (t70) cc_final: 0.7660 (t0) REVERT: A 675 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7024 (p0) REVERT: B 19 MET cc_start: 0.8013 (mmm) cc_final: 0.7754 (ttm) REVERT: B 24 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8086 (mp0) REVERT: B 25 GLU cc_start: 0.8700 (pp20) cc_final: 0.8160 (pp20) REVERT: B 60 MET cc_start: 0.8187 (tmm) cc_final: 0.7943 (tmm) REVERT: C 236 ASP cc_start: 0.8989 (t0) cc_final: 0.8768 (t0) REVERT: D 172 GLU cc_start: 0.8640 (pp20) cc_final: 0.8001 (pp20) REVERT: H 5 LYS cc_start: 0.7687 (mptt) cc_final: 0.6250 (tttp) REVERT: H 109 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8738 (mm-30) REVERT: H 142 HIS cc_start: 0.6629 (t-90) cc_final: 0.5667 (t-90) REVERT: H 181 GLU cc_start: 0.8455 (mp0) cc_final: 0.8044 (mp0) REVERT: H 188 ASN cc_start: 0.9206 (m-40) cc_final: 0.8884 (m-40) outliers start: 44 outliers final: 40 residues processed: 202 average time/residue: 0.2931 time to fit residues: 89.4956 Evaluate side-chains 207 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.0070 chunk 142 optimal weight: 4.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 198 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 = 0.3647 r_free = 0.3647 target = 0.096406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065319 restraints weight = 43916.017| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.68 r_work: 0.2865 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 17211 Z= 0.346 Angle : 0.978 59.199 23312 Z= 0.564 Chirality : 0.045 0.319 2625 Planarity : 0.005 0.076 2934 Dihedral : 8.259 97.036 2450 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.65 % Favored : 89.30 % Rotamer: Outliers : 2.43 % Allowed : 19.81 % Favored : 77.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.05 % 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: -1.46 (0.19), residues: 2020 helix: 0.90 (0.20), residues: 700 sheet: -0.35 (0.25), residues: 452 loop : -3.01 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 17 HIS 0.004 0.001 HIS A 860 PHE 0.026 0.001 PHE G 105 TYR 0.062 0.002 TYR G 136 ARG 0.010 0.000 ARG H 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.97 seconds wall clock time: 66 minutes 28.87 seconds (3988.87 seconds total)