Starting phenix.real_space_refine on Sun Mar 17 06:26:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iqw_9708/03_2024/6iqw_9708_updated.pdb" } resolution = 3.35 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= -0.008 sd= 1.289 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 26 5.49 5 S 50 5.16 5 C 10766 2.51 5 N 2947 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16935 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6131 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1094 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "C" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2113 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2177 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 24} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 11, 'rna3p': 12} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.41, per 1000 atoms: 0.56 Number of scatterers: 16935 At special positions: 0 Unit cell: (134.16, 147.68, 108.16, 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 50 16.00 P 26 15.00 O 3146 8.00 N 2947 7.00 C 10766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 274 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.8 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 14 sheets defined 34.3% alpha, 6.5% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.898A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.599A pdb=" N ALA A 23 " --> pdb=" O PRO A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.636A pdb=" N GLY A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.990A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.780A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 87 through 103 removed outlier: 4.072A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.808A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Proline residue: A 177 - end of helix removed outlier: 3.672A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 219 through 222 No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 256 through 281 removed outlier: 3.726A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 340 through 343 removed outlier: 3.502A pdb=" N PHE A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 351 through 368 Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.698A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.060A pdb=" N MET A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.843A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 562 through 565 No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 596 through 613 removed outlier: 3.988A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 4.107A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 removed outlier: 3.855A pdb=" N GLU A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.591A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.780A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 735 " --> pdb=" O TYR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 746 No H-bonds generated for 'chain 'A' and resid 743 through 746' Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 765 through 772 removed outlier: 4.442A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 71 through 87 removed outlier: 4.072A pdb=" N LEU B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 4.426A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.565A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 3.875A pdb=" N ARG B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 148 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 149 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.895A pdb=" N GLU B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 155 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 156 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.971A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.910A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.621A pdb=" N GLU C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 249 through 252 No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'C' and resid 268 through 271 No H-bonds generated for 'chain 'C' and resid 268 through 271' Processing helix chain 'C' and resid 277 through 286 removed outlier: 4.934A pdb=" N GLU C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.629A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.671A pdb=" N ASN D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 150 through 157 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.898A pdb=" N LYS D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 271 through 277 removed outlier: 4.361A pdb=" N SER D 274 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 276 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'E' and resid 46 through 49 No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 77 through 83 removed outlier: 4.176A pdb=" N THR E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY E 83 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 96 removed outlier: 3.521A pdb=" N ALA E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 172 through 178 removed outlier: 4.169A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 114 through 133 removed outlier: 3.984A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 removed outlier: 3.554A pdb=" N MET F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.792A pdb=" N ASP F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 181 through 187 Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 257 through 260 No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 281 through 304 removed outlier: 3.626A pdb=" N PHE F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET F 301 " --> pdb=" O TYR F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 322 Processing sheet with id= A, first strand: chain 'A' and resid 330 through 336 removed outlier: 3.767A pdb=" N PHE A 290 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 299 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 288 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 450 through 454 removed outlier: 3.968A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN A 481 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 467 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 483 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 620 through 627 removed outlier: 4.058A pdb=" N PHE A 590 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 9 through 13 Processing sheet with id= E, first strand: chain 'C' and resid 15 through 17 Processing sheet with id= F, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= G, first strand: chain 'D' and resid 9 through 11 Processing sheet with id= H, first strand: chain 'D' and resid 167 through 169 Processing sheet with id= I, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.567A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 3 through 6 Processing sheet with id= K, first strand: chain 'F' and resid 209 through 211 Processing sheet with id= L, first strand: chain 'F' and resid 222 through 227 removed outlier: 4.706A pdb=" N ILE F 238 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 331 through 334 Processing sheet with id= N, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.887A pdb=" N TYR F 85 " --> pdb=" O VAL F 34 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3929 1.33 - 1.45: 3922 1.45 - 1.57: 9395 1.57 - 1.69: 51 1.69 - 1.82: 82 Bond restraints: 17379 Sorted by residual: bond pdb=" C LEU F 20 " pdb=" N THR F 21 " ideal model delta sigma weight residual 1.331 1.207 0.124 1.59e-02 3.96e+03 6.11e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.65e+01 bond pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 1.459 1.400 0.059 1.16e-02 7.43e+03 2.56e+01 bond pdb=" C5 ATP A 801 " pdb=" N7 ATP A 801 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.60: 495 105.60 - 113.18: 9201 113.18 - 120.76: 8284 120.76 - 128.34: 5456 128.34 - 135.92: 179 Bond angle restraints: 23615 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 119.70 17.13 1.00e+00 1.00e+00 2.93e+02 angle pdb=" C GLU E 88 " pdb=" N ARG E 89 " pdb=" CA ARG E 89 " ideal model delta sigma weight residual 120.79 108.58 12.21 1.39e+00 5.18e-01 7.71e+01 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.56 8.24 1.00e+00 1.00e+00 6.79e+01 angle pdb=" N3 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N9 ATP A 801 " ideal model delta sigma weight residual 127.04 135.05 -8.01 1.15e+00 7.59e-01 4.87e+01 ... (remaining 23610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.01: 9107 19.01 - 38.02: 1065 38.02 - 57.03: 196 57.03 - 76.03: 51 76.03 - 95.04: 2 Dihedral angle restraints: 10421 sinusoidal: 4478 harmonic: 5943 Sorted by residual: dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N GLU A 326 " pdb=" CA GLU A 326 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA VAL D 39 " pdb=" C VAL D 39 " pdb=" N ILE D 40 " pdb=" CA ILE D 40 " ideal model delta harmonic sigma weight residual -180.00 -146.38 -33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ARG A 394 " pdb=" C ARG A 394 " pdb=" N GLU A 395 " pdb=" CA GLU A 395 " ideal model delta harmonic sigma weight residual 180.00 146.74 33.26 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 10418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1886 0.060 - 0.119: 548 0.119 - 0.179: 119 0.179 - 0.238: 14 0.238 - 0.298: 4 Chirality restraints: 2571 Sorted by residual: chirality pdb=" C1' A I 18 " pdb=" O4' A I 18 " pdb=" C2' A I 18 " pdb=" N9 A I 18 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE D 196 " pdb=" CA ILE D 196 " pdb=" CG1 ILE D 196 " pdb=" CG2 ILE D 196 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE C 15 " pdb=" CA ILE C 15 " pdb=" CG1 ILE C 15 " pdb=" CG2 ILE C 15 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2568 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 141 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C SER E 141 " 0.068 2.00e-02 2.50e+03 pdb=" O SER E 141 " -0.025 2.00e-02 2.50e+03 pdb=" N SER E 142 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 58 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO E 59 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 59 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 59 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 494 " -0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 495 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.046 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 48 2.39 - 3.01: 8742 3.01 - 3.64: 26097 3.64 - 4.27: 38714 4.27 - 4.90: 62731 Nonbonded interactions: 136332 Sorted by model distance: nonbonded pdb=" O ALA B 51 " pdb=" CD2 TYR B 55 " model vdw 1.757 3.340 nonbonded pdb=" O ARG E 89 " pdb=" OG1 THR E 92 " model vdw 2.168 2.440 nonbonded pdb=" O GLY F 15 " pdb=" O2' C I 21 " model vdw 2.210 2.440 nonbonded pdb=" O GLU E 88 " pdb=" O ARG E 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 727 " pdb=" O GLN B 173 " model vdw 2.254 2.440 ... (remaining 136327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 4 through 25 or resid 38 through 194 or (resid 195 and (na \ me N or name CA or name C or name O or name CB )) or resid 196 through 282)) selection = (chain 'D' and (resid 4 through 25 or resid 38 through 63 or (resid 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 223 or (resi \ d 224 and (name N or name CA or name C or name O or name CB )) or resid 225 thro \ ugh 234 or (resid 235 and (name N or name CA or name C or name O or name CB )) o \ r resid 236 through 282)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 3.960 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 49.160 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.007 0.124 17379 Z= 0.445 Angle : 1.051 19.035 23615 Z= 0.594 Chirality : 0.059 0.298 2571 Planarity : 0.008 0.090 2941 Dihedral : 16.456 95.044 6622 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.52 % Favored : 86.09 % Rotamer: Outliers : 0.35 % Allowed : 10.34 % Favored : 89.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.25 % 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: -4.93 (0.14), residues: 2049 helix: -3.21 (0.12), residues: 730 sheet: -3.15 (0.34), residues: 185 loop : -3.44 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 131 HIS 0.009 0.002 HIS A 60 PHE 0.038 0.003 PHE E 159 TYR 0.031 0.003 TYR E 272 ARG 0.014 0.001 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 678 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6145 (m-80) cc_final: 0.4458 (m-80) REVERT: A 36 ARG cc_start: 0.8522 (tpt90) cc_final: 0.8135 (tpt90) REVERT: A 99 GLU cc_start: 0.8918 (tp30) cc_final: 0.8275 (tp30) REVERT: A 114 GLN cc_start: 0.8173 (pt0) cc_final: 0.7249 (mp10) REVERT: A 121 SER cc_start: 0.9111 (t) cc_final: 0.8782 (m) REVERT: A 169 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6610 (mtmm) REVERT: A 181 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8438 (ptmm) REVERT: A 192 GLU cc_start: 0.8343 (tt0) cc_final: 0.8004 (pm20) REVERT: A 199 TYR cc_start: 0.8822 (t80) cc_final: 0.8314 (t80) REVERT: A 200 ASP cc_start: 0.8518 (m-30) cc_final: 0.8244 (m-30) REVERT: A 204 MET cc_start: 0.9359 (mmp) cc_final: 0.9113 (mmt) REVERT: A 237 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 241 SER cc_start: 0.9125 (t) cc_final: 0.8639 (p) REVERT: A 272 ASP cc_start: 0.8512 (t0) cc_final: 0.7973 (t70) REVERT: A 276 GLU cc_start: 0.7941 (tp30) cc_final: 0.7482 (tp30) REVERT: A 283 LEU cc_start: 0.9398 (mt) cc_final: 0.9012 (mp) REVERT: A 287 ASN cc_start: 0.9168 (m110) cc_final: 0.8201 (m110) REVERT: A 299 ILE cc_start: 0.9406 (mt) cc_final: 0.8999 (mt) REVERT: A 301 GLN cc_start: 0.8876 (pm20) cc_final: 0.8521 (pm20) REVERT: A 359 LEU cc_start: 0.9225 (tp) cc_final: 0.8101 (tp) REVERT: A 430 LEU cc_start: 0.7981 (mt) cc_final: 0.7716 (tp) REVERT: A 435 THR cc_start: 0.8718 (t) cc_final: 0.8252 (p) REVERT: A 454 TYR cc_start: 0.7905 (t80) cc_final: 0.6925 (t80) REVERT: A 464 GLN cc_start: 0.8708 (mp10) cc_final: 0.7826 (mp10) REVERT: A 490 TYR cc_start: 0.8071 (t80) cc_final: 0.7318 (t80) REVERT: A 503 GLU cc_start: 0.8563 (tt0) cc_final: 0.8138 (mt-10) REVERT: A 513 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8054 (ttm-80) REVERT: A 550 LYS cc_start: 0.8316 (mttt) cc_final: 0.7970 (mttm) REVERT: A 629 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6545 (mt-10) REVERT: A 638 ASP cc_start: 0.8348 (m-30) cc_final: 0.7837 (t0) REVERT: A 664 LEU cc_start: 0.8889 (mt) cc_final: 0.8687 (mp) REVERT: A 708 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8370 (mmtp) REVERT: A 725 TRP cc_start: 0.9004 (p-90) cc_final: 0.7564 (p-90) REVERT: A 745 LEU cc_start: 0.8413 (mt) cc_final: 0.7948 (mt) REVERT: A 762 TYR cc_start: 0.8413 (t80) cc_final: 0.8048 (t80) REVERT: B 74 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8186 (mtm-85) REVERT: B 86 THR cc_start: 0.9324 (t) cc_final: 0.9104 (p) REVERT: B 97 LYS cc_start: 0.8808 (tptp) cc_final: 0.8269 (mttm) REVERT: B 122 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8451 (mmmm) REVERT: B 129 TYR cc_start: 0.8663 (t80) cc_final: 0.8311 (t80) REVERT: C 14 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7724 (mtpp) REVERT: C 68 ASN cc_start: 0.8968 (t0) cc_final: 0.8663 (t0) REVERT: C 94 GLN cc_start: 0.7616 (mt0) cc_final: 0.7069 (mm-40) REVERT: C 95 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7580 (mp0) REVERT: C 106 ASN cc_start: 0.8219 (t0) cc_final: 0.7800 (t0) REVERT: C 142 ILE cc_start: 0.8590 (mt) cc_final: 0.8371 (mm) REVERT: C 143 VAL cc_start: 0.9042 (t) cc_final: 0.8841 (t) REVERT: C 183 ASN cc_start: 0.8700 (m-40) cc_final: 0.7543 (m-40) REVERT: C 237 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7992 (ttpp) REVERT: C 249 ASP cc_start: 0.6923 (t70) cc_final: 0.6397 (t0) REVERT: D 70 ARG cc_start: 0.7491 (mmm160) cc_final: 0.7155 (mmp80) REVERT: D 136 ASN cc_start: 0.8586 (m110) cc_final: 0.8280 (m110) REVERT: D 202 ASN cc_start: 0.8138 (m-40) cc_final: 0.7886 (p0) REVERT: E 43 GLU cc_start: 0.7733 (tm-30) cc_final: 0.6989 (mt-10) REVERT: E 63 ASP cc_start: 0.8698 (p0) cc_final: 0.8486 (p0) REVERT: E 105 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8024 (mtpp) REVERT: E 128 ASP cc_start: 0.8255 (t0) cc_final: 0.7738 (t0) REVERT: E 148 GLU cc_start: 0.7371 (mp0) cc_final: 0.6715 (mt-10) REVERT: E 200 HIS cc_start: 0.7972 (t-170) cc_final: 0.7435 (t70) REVERT: E 262 ARG cc_start: 0.6698 (mtt-85) cc_final: 0.5945 (mtt180) REVERT: F 36 ASP cc_start: 0.8474 (t0) cc_final: 0.8241 (t0) REVERT: F 86 THR cc_start: 0.9104 (p) cc_final: 0.8774 (t) REVERT: F 98 MET cc_start: 0.5745 (mtt) cc_final: 0.5410 (mpp) REVERT: F 163 TYR cc_start: 0.8294 (t80) cc_final: 0.7751 (t80) REVERT: F 220 LYS cc_start: 0.8495 (pttt) cc_final: 0.7769 (ttpt) REVERT: F 275 LEU cc_start: 0.8864 (mt) cc_final: 0.8302 (tt) REVERT: F 290 TRP cc_start: 0.8578 (m100) cc_final: 0.8266 (m100) REVERT: F 297 TYR cc_start: 0.7358 (m-80) cc_final: 0.6890 (m-80) REVERT: F 298 THR cc_start: 0.8774 (m) cc_final: 0.8464 (p) REVERT: F 319 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8734 (mmt-90) REVERT: F 385 LEU cc_start: 0.8343 (mt) cc_final: 0.7784 (tp) REVERT: F 389 MET cc_start: 0.7573 (mpp) cc_final: 0.7176 (mpp) outliers start: 6 outliers final: 3 residues processed: 680 average time/residue: 0.3201 time to fit residues: 318.4882 Evaluate side-chains 484 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 481 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain F residue 305 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 162 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 187 optimal weight: 40.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 124 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 205 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17379 Z= 0.305 Angle : 0.754 11.458 23615 Z= 0.392 Chirality : 0.049 0.315 2571 Planarity : 0.006 0.078 2941 Dihedral : 12.440 93.608 2704 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.69 % Favored : 87.07 % Rotamer: Outliers : 5.20 % Allowed : 20.15 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.84 (0.16), residues: 2049 helix: -1.77 (0.16), residues: 744 sheet: -2.72 (0.34), residues: 189 loop : -3.18 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 206 HIS 0.009 0.001 HIS C 44 PHE 0.022 0.002 PHE C 128 TYR 0.033 0.002 TYR B 55 ARG 0.009 0.001 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 493 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6155 (m-80) cc_final: 0.5246 (m-80) REVERT: A 65 MET cc_start: 0.7345 (mtt) cc_final: 0.7067 (mtt) REVERT: A 71 MET cc_start: 0.8292 (tpt) cc_final: 0.7784 (tpt) REVERT: A 99 GLU cc_start: 0.8839 (tp30) cc_final: 0.8307 (tp30) REVERT: A 114 GLN cc_start: 0.8155 (pt0) cc_final: 0.7346 (mp10) REVERT: A 121 SER cc_start: 0.9238 (t) cc_final: 0.8850 (m) REVERT: A 152 GLN cc_start: 0.8269 (pt0) cc_final: 0.7193 (tp40) REVERT: A 169 LYS cc_start: 0.7355 (mtpp) cc_final: 0.6682 (mtmm) REVERT: A 192 GLU cc_start: 0.8501 (tt0) cc_final: 0.8201 (pm20) REVERT: A 203 ARG cc_start: 0.9088 (ttm170) cc_final: 0.8798 (ptm-80) REVERT: A 237 GLU cc_start: 0.7911 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 253 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8734 (mmmt) REVERT: A 272 ASP cc_start: 0.8603 (t0) cc_final: 0.8069 (t70) REVERT: A 276 GLU cc_start: 0.8069 (tp30) cc_final: 0.7485 (tp30) REVERT: A 287 ASN cc_start: 0.9151 (m110) cc_final: 0.8641 (m-40) REVERT: A 299 ILE cc_start: 0.9365 (mt) cc_final: 0.9133 (mt) REVERT: A 359 LEU cc_start: 0.9250 (tp) cc_final: 0.8129 (tp) REVERT: A 430 LEU cc_start: 0.7946 (mt) cc_final: 0.7727 (tp) REVERT: A 435 THR cc_start: 0.8733 (t) cc_final: 0.8270 (p) REVERT: A 454 TYR cc_start: 0.8041 (t80) cc_final: 0.7106 (t80) REVERT: A 464 GLN cc_start: 0.8591 (mp10) cc_final: 0.7756 (mp10) REVERT: A 490 TYR cc_start: 0.8091 (t80) cc_final: 0.7372 (t80) REVERT: A 503 GLU cc_start: 0.8670 (tt0) cc_final: 0.8189 (mt-10) REVERT: A 513 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8075 (ttm-80) REVERT: A 549 PHE cc_start: 0.8802 (m-80) cc_final: 0.8558 (m-80) REVERT: A 550 LYS cc_start: 0.8219 (mttt) cc_final: 0.7936 (mttm) REVERT: A 577 GLU cc_start: 0.7395 (tt0) cc_final: 0.6772 (pp20) REVERT: A 588 ASP cc_start: 0.8437 (p0) cc_final: 0.8185 (p0) REVERT: A 629 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6482 (mt-10) REVERT: A 638 ASP cc_start: 0.8390 (m-30) cc_final: 0.7935 (t0) REVERT: A 715 LEU cc_start: 0.9021 (mt) cc_final: 0.8709 (mt) REVERT: A 724 ARG cc_start: 0.8651 (mtp180) cc_final: 0.7503 (mmp-170) REVERT: A 725 TRP cc_start: 0.9097 (p-90) cc_final: 0.7560 (p-90) REVERT: A 745 LEU cc_start: 0.8374 (mt) cc_final: 0.7875 (mp) REVERT: B 96 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7156 (tpp-160) REVERT: B 97 LYS cc_start: 0.8834 (tptp) cc_final: 0.8546 (mttm) REVERT: B 122 LYS cc_start: 0.9305 (ptpt) cc_final: 0.8390 (mmmm) REVERT: B 123 MET cc_start: 0.9337 (mtp) cc_final: 0.9046 (ttm) REVERT: B 133 LYS cc_start: 0.8512 (tptp) cc_final: 0.8143 (ptmt) REVERT: B 157 MET cc_start: 0.8267 (tpp) cc_final: 0.8009 (tpt) REVERT: C 12 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8110 (ttmt) REVERT: C 14 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7679 (mtpp) REVERT: C 68 ASN cc_start: 0.8989 (t0) cc_final: 0.8778 (t0) REVERT: C 85 SER cc_start: 0.8858 (m) cc_final: 0.8564 (p) REVERT: C 89 CYS cc_start: 0.7807 (m) cc_final: 0.7568 (m) REVERT: C 94 GLN cc_start: 0.7612 (mt0) cc_final: 0.7140 (mm-40) REVERT: C 95 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7860 (mp0) REVERT: C 106 ASN cc_start: 0.8177 (t0) cc_final: 0.7765 (t0) REVERT: C 127 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 142 ILE cc_start: 0.8763 (mt) cc_final: 0.8550 (mm) REVERT: C 237 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8128 (ttpp) REVERT: D 47 LEU cc_start: 0.8834 (mt) cc_final: 0.8633 (mt) REVERT: D 70 ARG cc_start: 0.7398 (mmm160) cc_final: 0.6992 (mmt90) REVERT: D 183 ASN cc_start: 0.8845 (m-40) cc_final: 0.8616 (m110) REVERT: E 20 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8267 (tpm170) REVERT: E 43 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7436 (mt-10) REVERT: E 63 ASP cc_start: 0.8653 (p0) cc_final: 0.8367 (p0) REVERT: E 86 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7631 (tp30) REVERT: E 124 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: E 200 HIS cc_start: 0.7907 (t-170) cc_final: 0.7415 (t70) REVERT: E 237 PHE cc_start: 0.8052 (m-80) cc_final: 0.7591 (m-10) REVERT: E 264 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7603 (mm-30) REVERT: F 36 ASP cc_start: 0.8581 (t0) cc_final: 0.8353 (t0) REVERT: F 86 THR cc_start: 0.9023 (p) cc_final: 0.8804 (t) REVERT: F 131 LYS cc_start: 0.8257 (tttp) cc_final: 0.7549 (tppt) REVERT: F 163 TYR cc_start: 0.8306 (t80) cc_final: 0.7794 (t80) REVERT: F 183 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: F 204 ASP cc_start: 0.9050 (t0) cc_final: 0.8466 (t0) REVERT: F 220 LYS cc_start: 0.8551 (pttt) cc_final: 0.7898 (ttpt) REVERT: F 275 LEU cc_start: 0.8820 (mt) cc_final: 0.8435 (tt) REVERT: F 290 TRP cc_start: 0.8608 (m100) cc_final: 0.8404 (m100) REVERT: F 297 TYR cc_start: 0.7523 (m-80) cc_final: 0.7058 (m-80) REVERT: F 319 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8757 (mmt-90) REVERT: F 385 LEU cc_start: 0.8346 (mt) cc_final: 0.7656 (pp) outliers start: 89 outliers final: 66 residues processed: 536 average time/residue: 0.3134 time to fit residues: 246.6328 Evaluate side-chains 523 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 454 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 0.0870 chunk 128 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 212 ASN F 13 HIS F 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17379 Z= 0.324 Angle : 0.733 12.035 23615 Z= 0.381 Chirality : 0.049 0.305 2571 Planarity : 0.006 0.088 2941 Dihedral : 12.257 90.428 2704 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.47 % Favored : 86.33 % Rotamer: Outliers : 6.95 % Allowed : 22.14 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.34 (0.17), residues: 2049 helix: -1.16 (0.17), residues: 755 sheet: -2.42 (0.34), residues: 192 loop : -3.07 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 206 HIS 0.006 0.001 HIS A 60 PHE 0.029 0.002 PHE E 116 TYR 0.034 0.002 TYR B 55 ARG 0.008 0.001 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 477 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7187 (mtt) cc_final: 0.6866 (mtt) REVERT: A 71 MET cc_start: 0.8229 (tpt) cc_final: 0.7707 (tpt) REVERT: A 99 GLU cc_start: 0.8800 (tp30) cc_final: 0.8312 (tp30) REVERT: A 114 GLN cc_start: 0.8165 (pt0) cc_final: 0.7367 (mp10) REVERT: A 121 SER cc_start: 0.9256 (t) cc_final: 0.8817 (m) REVERT: A 152 GLN cc_start: 0.8274 (pt0) cc_final: 0.7177 (tp40) REVERT: A 181 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8461 (ptmm) REVERT: A 192 GLU cc_start: 0.8535 (tt0) cc_final: 0.8256 (pm20) REVERT: A 203 ARG cc_start: 0.9203 (ttm170) cc_final: 0.8878 (ptm-80) REVERT: A 237 GLU cc_start: 0.7881 (mt-10) cc_final: 0.6834 (mt-10) REVERT: A 245 ASP cc_start: 0.8799 (m-30) cc_final: 0.8218 (t0) REVERT: A 253 LYS cc_start: 0.8996 (mmtp) cc_final: 0.8783 (mmmt) REVERT: A 272 ASP cc_start: 0.8579 (t0) cc_final: 0.8030 (t70) REVERT: A 276 GLU cc_start: 0.8059 (tp30) cc_final: 0.7554 (tp30) REVERT: A 287 ASN cc_start: 0.9203 (m110) cc_final: 0.8673 (m-40) REVERT: A 299 ILE cc_start: 0.9356 (mt) cc_final: 0.9031 (mt) REVERT: A 359 LEU cc_start: 0.9247 (tp) cc_final: 0.8138 (tp) REVERT: A 435 THR cc_start: 0.8782 (t) cc_final: 0.8046 (p) REVERT: A 439 ASP cc_start: 0.7812 (m-30) cc_final: 0.7334 (m-30) REVERT: A 464 GLN cc_start: 0.8601 (mp10) cc_final: 0.7865 (mp10) REVERT: A 490 TYR cc_start: 0.7993 (t80) cc_final: 0.7368 (t80) REVERT: A 513 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8092 (ttm-80) REVERT: A 537 LYS cc_start: 0.8805 (mttt) cc_final: 0.8485 (mttp) REVERT: A 550 LYS cc_start: 0.8147 (mttt) cc_final: 0.7886 (mttm) REVERT: A 560 LYS cc_start: 0.8596 (mttp) cc_final: 0.8162 (mmmt) REVERT: A 577 GLU cc_start: 0.7390 (tt0) cc_final: 0.6420 (tt0) REVERT: A 588 ASP cc_start: 0.8463 (p0) cc_final: 0.8219 (p0) REVERT: A 629 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6502 (mt-10) REVERT: A 638 ASP cc_start: 0.8403 (m-30) cc_final: 0.7972 (t0) REVERT: A 650 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 715 LEU cc_start: 0.9033 (mt) cc_final: 0.8719 (mt) REVERT: A 718 ARG cc_start: 0.8355 (ttm170) cc_final: 0.7766 (mtp180) REVERT: A 724 ARG cc_start: 0.8657 (mtp180) cc_final: 0.7448 (mmp-170) REVERT: A 725 TRP cc_start: 0.9125 (p-90) cc_final: 0.7596 (p-90) REVERT: A 745 LEU cc_start: 0.8394 (mt) cc_final: 0.7757 (mt) REVERT: A 751 LYS cc_start: 0.8766 (mmtm) cc_final: 0.8543 (mmtm) REVERT: B 96 ARG cc_start: 0.7713 (ttm110) cc_final: 0.6828 (tpp-160) REVERT: B 97 LYS cc_start: 0.8756 (tptp) cc_final: 0.8443 (mttm) REVERT: B 103 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7177 (mtt180) REVERT: B 122 LYS cc_start: 0.9301 (ptpt) cc_final: 0.8412 (mmmm) REVERT: B 123 MET cc_start: 0.9267 (mtp) cc_final: 0.8997 (ttm) REVERT: C 14 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7719 (mtpp) REVERT: C 68 ASN cc_start: 0.9068 (t0) cc_final: 0.8864 (t0) REVERT: C 85 SER cc_start: 0.8932 (m) cc_final: 0.8666 (p) REVERT: C 89 CYS cc_start: 0.7868 (m) cc_final: 0.7582 (m) REVERT: C 94 GLN cc_start: 0.7597 (mt0) cc_final: 0.7148 (mm-40) REVERT: C 95 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7823 (mp0) REVERT: C 106 ASN cc_start: 0.8282 (t0) cc_final: 0.7914 (t0) REVERT: C 127 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9028 (tt) REVERT: C 195 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7197 (tt0) REVERT: C 237 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8133 (ttpp) REVERT: C 259 ILE cc_start: 0.8053 (mp) cc_final: 0.7713 (mt) REVERT: D 70 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7127 (mpt-90) REVERT: D 115 ASP cc_start: 0.8210 (t0) cc_final: 0.7899 (t70) REVERT: D 250 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6483 (p90) REVERT: D 267 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.5937 (mtpp) REVERT: E 43 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7489 (mt-10) REVERT: E 63 ASP cc_start: 0.8612 (p0) cc_final: 0.8317 (p0) REVERT: E 86 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7499 (tp30) REVERT: E 118 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8995 (mt) REVERT: E 124 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6876 (m-10) REVERT: E 200 HIS cc_start: 0.7979 (t-170) cc_final: 0.7503 (t70) REVERT: E 237 PHE cc_start: 0.8064 (m-80) cc_final: 0.7594 (m-10) REVERT: E 262 ARG cc_start: 0.7229 (ttm170) cc_final: 0.6964 (ttm170) REVERT: E 264 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 36 ASP cc_start: 0.8643 (t0) cc_final: 0.8429 (t0) REVERT: F 86 THR cc_start: 0.9059 (p) cc_final: 0.8732 (m) REVERT: F 131 LYS cc_start: 0.8294 (tttp) cc_final: 0.7576 (tppt) REVERT: F 163 TYR cc_start: 0.8304 (t80) cc_final: 0.7793 (t80) REVERT: F 183 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: F 204 ASP cc_start: 0.8974 (t0) cc_final: 0.8415 (t0) REVERT: F 220 LYS cc_start: 0.8549 (pttt) cc_final: 0.7934 (ttpt) REVERT: F 275 LEU cc_start: 0.8804 (mt) cc_final: 0.8458 (tt) REVERT: F 290 TRP cc_start: 0.8746 (m100) cc_final: 0.8417 (m100) REVERT: F 297 TYR cc_start: 0.7595 (m-80) cc_final: 0.7143 (m-80) REVERT: F 319 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8733 (mmt-90) REVERT: F 327 ASP cc_start: 0.6929 (t0) cc_final: 0.6401 (p0) REVERT: F 385 LEU cc_start: 0.8358 (mt) cc_final: 0.7603 (pp) outliers start: 119 outliers final: 85 residues processed: 537 average time/residue: 0.2919 time to fit residues: 232.1400 Evaluate side-chains 541 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 449 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 598 GLN B 88 GLN B 179 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS F 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17379 Z= 0.262 Angle : 0.696 12.237 23615 Z= 0.358 Chirality : 0.048 0.286 2571 Planarity : 0.006 0.088 2941 Dihedral : 12.059 87.942 2704 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.74 % Favored : 87.12 % Rotamer: Outliers : 7.01 % Allowed : 24.01 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.99 (0.17), residues: 2049 helix: -0.78 (0.18), residues: 749 sheet: -2.33 (0.35), residues: 196 loop : -2.89 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.006 0.001 HIS A 60 PHE 0.023 0.002 PHE D 238 TYR 0.030 0.002 TYR B 55 ARG 0.007 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 471 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6973 (mtt) cc_final: 0.6675 (mtt) REVERT: A 71 MET cc_start: 0.8294 (tpt) cc_final: 0.7795 (tpt) REVERT: A 99 GLU cc_start: 0.8830 (tp30) cc_final: 0.8334 (tp30) REVERT: A 114 GLN cc_start: 0.8071 (pt0) cc_final: 0.7331 (mp10) REVERT: A 121 SER cc_start: 0.9208 (t) cc_final: 0.8701 (m) REVERT: A 152 GLN cc_start: 0.8268 (pt0) cc_final: 0.7318 (tp40) REVERT: A 181 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8536 (ptmm) REVERT: A 192 GLU cc_start: 0.8468 (tt0) cc_final: 0.8223 (pm20) REVERT: A 203 ARG cc_start: 0.9168 (ttm170) cc_final: 0.8947 (ptm-80) REVERT: A 237 GLU cc_start: 0.7849 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 245 ASP cc_start: 0.8743 (m-30) cc_final: 0.8308 (t0) REVERT: A 249 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7860 (ttm-80) REVERT: A 253 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8782 (mmmt) REVERT: A 272 ASP cc_start: 0.8522 (t0) cc_final: 0.8070 (t70) REVERT: A 287 ASN cc_start: 0.9200 (m110) cc_final: 0.8687 (m-40) REVERT: A 299 ILE cc_start: 0.9302 (mt) cc_final: 0.9088 (mt) REVERT: A 359 LEU cc_start: 0.9211 (tp) cc_final: 0.8091 (tp) REVERT: A 435 THR cc_start: 0.8778 (t) cc_final: 0.8067 (p) REVERT: A 439 ASP cc_start: 0.7828 (m-30) cc_final: 0.7349 (m-30) REVERT: A 464 GLN cc_start: 0.8585 (mp10) cc_final: 0.7914 (mp10) REVERT: A 490 TYR cc_start: 0.7921 (t80) cc_final: 0.7270 (t80) REVERT: A 513 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8032 (ttm-80) REVERT: A 537 LYS cc_start: 0.8849 (mttt) cc_final: 0.8621 (mttp) REVERT: A 560 LYS cc_start: 0.8593 (mttp) cc_final: 0.8191 (mmmt) REVERT: A 601 GLU cc_start: 0.8136 (tt0) cc_final: 0.7908 (tt0) REVERT: A 629 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6458 (mt-10) REVERT: A 638 ASP cc_start: 0.8413 (m-30) cc_final: 0.7899 (t0) REVERT: A 715 LEU cc_start: 0.9052 (mt) cc_final: 0.8726 (mt) REVERT: A 718 ARG cc_start: 0.8369 (ttm170) cc_final: 0.7932 (mtp180) REVERT: A 724 ARG cc_start: 0.8634 (mtp180) cc_final: 0.7415 (mmp-170) REVERT: A 725 TRP cc_start: 0.9124 (p-90) cc_final: 0.7586 (p-90) REVERT: A 745 LEU cc_start: 0.8421 (mt) cc_final: 0.7839 (mp) REVERT: A 751 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8572 (mmtm) REVERT: B 96 ARG cc_start: 0.7719 (ttm110) cc_final: 0.6902 (mmp-170) REVERT: B 97 LYS cc_start: 0.8724 (tptp) cc_final: 0.8400 (mttm) REVERT: B 122 LYS cc_start: 0.9261 (ptpt) cc_final: 0.8437 (mmmt) REVERT: B 123 MET cc_start: 0.9200 (mtp) cc_final: 0.8898 (ttm) REVERT: B 133 LYS cc_start: 0.8681 (tptp) cc_final: 0.8274 (ptmt) REVERT: C 14 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7713 (mtpp) REVERT: C 85 SER cc_start: 0.8909 (m) cc_final: 0.8642 (p) REVERT: C 89 CYS cc_start: 0.7826 (m) cc_final: 0.7503 (m) REVERT: C 94 GLN cc_start: 0.7583 (mt0) cc_final: 0.7099 (tp40) REVERT: C 95 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7741 (mp0) REVERT: C 106 ASN cc_start: 0.8236 (t0) cc_final: 0.7853 (t0) REVERT: C 133 LYS cc_start: 0.8635 (tptt) cc_final: 0.8067 (ptpp) REVERT: C 195 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7295 (tt0) REVERT: C 237 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8156 (ttpp) REVERT: C 259 ILE cc_start: 0.7991 (mp) cc_final: 0.7678 (mt) REVERT: D 47 LEU cc_start: 0.8904 (mt) cc_final: 0.8659 (mt) REVERT: D 70 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7192 (mpt-90) REVERT: D 115 ASP cc_start: 0.8155 (t0) cc_final: 0.7896 (t70) REVERT: D 180 PRO cc_start: 0.9143 (Cg_endo) cc_final: 0.8844 (Cg_exo) REVERT: D 202 ASN cc_start: 0.8272 (m-40) cc_final: 0.7939 (t0) REVERT: E 43 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7497 (mt-10) REVERT: E 63 ASP cc_start: 0.8574 (p0) cc_final: 0.8298 (p0) REVERT: E 86 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7426 (tp30) REVERT: E 118 ILE cc_start: 0.9398 (tp) cc_final: 0.9082 (mt) REVERT: E 124 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6839 (m-10) REVERT: E 200 HIS cc_start: 0.7907 (t-170) cc_final: 0.7517 (t70) REVERT: E 202 MET cc_start: 0.8339 (mmm) cc_final: 0.7593 (ttt) REVERT: E 237 PHE cc_start: 0.7992 (m-80) cc_final: 0.7496 (m-10) REVERT: E 262 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7209 (ttm170) REVERT: F 23 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (p) REVERT: F 36 ASP cc_start: 0.8651 (t0) cc_final: 0.8431 (t0) REVERT: F 45 MET cc_start: 0.6221 (mmm) cc_final: 0.5609 (mtm) REVERT: F 86 THR cc_start: 0.9060 (p) cc_final: 0.8784 (m) REVERT: F 131 LYS cc_start: 0.8307 (tttp) cc_final: 0.7572 (tppt) REVERT: F 183 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: F 220 LYS cc_start: 0.8532 (pttt) cc_final: 0.7929 (ttpt) REVERT: F 275 LEU cc_start: 0.8814 (mt) cc_final: 0.8471 (tt) REVERT: F 290 TRP cc_start: 0.8822 (m100) cc_final: 0.8489 (m100) REVERT: F 297 TYR cc_start: 0.7712 (m-80) cc_final: 0.7171 (m-80) REVERT: F 319 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8727 (mmt-90) REVERT: F 327 ASP cc_start: 0.6979 (t0) cc_final: 0.6420 (p0) outliers start: 120 outliers final: 93 residues processed: 532 average time/residue: 0.2971 time to fit residues: 232.7004 Evaluate side-chains 540 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 444 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 17379 Z= 0.484 Angle : 0.827 14.278 23615 Z= 0.426 Chirality : 0.051 0.295 2571 Planarity : 0.006 0.078 2941 Dihedral : 12.244 84.420 2703 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.15 % Favored : 85.65 % Rotamer: Outliers : 9.05 % Allowed : 24.24 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.18), residues: 2049 helix: -0.79 (0.18), residues: 746 sheet: -2.49 (0.32), residues: 218 loop : -2.91 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 235 HIS 0.019 0.002 HIS F 13 PHE 0.032 0.003 PHE C 101 TYR 0.030 0.003 TYR F 303 ARG 0.009 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 442 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6987 (mtt) cc_final: 0.6718 (mmm) REVERT: A 71 MET cc_start: 0.8300 (tpt) cc_final: 0.7760 (tpt) REVERT: A 99 GLU cc_start: 0.8848 (tp30) cc_final: 0.8412 (tp30) REVERT: A 114 GLN cc_start: 0.8147 (pt0) cc_final: 0.7485 (mp10) REVERT: A 121 SER cc_start: 0.9234 (t) cc_final: 0.8715 (m) REVERT: A 152 GLN cc_start: 0.8266 (pt0) cc_final: 0.7469 (tp40) REVERT: A 166 SER cc_start: 0.8474 (m) cc_final: 0.8124 (p) REVERT: A 181 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8404 (ptmm) REVERT: A 192 GLU cc_start: 0.8667 (tt0) cc_final: 0.8374 (pm20) REVERT: A 237 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 245 ASP cc_start: 0.8820 (m-30) cc_final: 0.8356 (t0) REVERT: A 249 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: A 253 LYS cc_start: 0.9073 (mmtp) cc_final: 0.8872 (mmmt) REVERT: A 272 ASP cc_start: 0.8595 (t0) cc_final: 0.8197 (t0) REVERT: A 276 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 330 TYR cc_start: 0.9420 (t80) cc_final: 0.9166 (t80) REVERT: A 359 LEU cc_start: 0.9245 (tp) cc_final: 0.8349 (tp) REVERT: A 435 THR cc_start: 0.8872 (t) cc_final: 0.8100 (p) REVERT: A 439 ASP cc_start: 0.7905 (m-30) cc_final: 0.7361 (m-30) REVERT: A 464 GLN cc_start: 0.8600 (mp10) cc_final: 0.7869 (mp10) REVERT: A 490 TYR cc_start: 0.8098 (t80) cc_final: 0.7426 (t80) REVERT: A 492 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7570 (tppt) REVERT: A 513 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8079 (ttm-80) REVERT: A 537 LYS cc_start: 0.8850 (mttt) cc_final: 0.8618 (mttp) REVERT: A 577 GLU cc_start: 0.7050 (tt0) cc_final: 0.6838 (tt0) REVERT: A 629 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6470 (mt-10) REVERT: A 638 ASP cc_start: 0.8429 (m-30) cc_final: 0.7975 (t0) REVERT: A 707 TRP cc_start: 0.8513 (m100) cc_final: 0.8116 (m100) REVERT: A 718 ARG cc_start: 0.8338 (ttm170) cc_final: 0.7848 (mtp180) REVERT: A 724 ARG cc_start: 0.8696 (mtp180) cc_final: 0.7512 (mmp-170) REVERT: B 96 ARG cc_start: 0.7781 (ttm110) cc_final: 0.6820 (tpp-160) REVERT: B 97 LYS cc_start: 0.8773 (tptp) cc_final: 0.8445 (mttp) REVERT: B 122 LYS cc_start: 0.9254 (ptpt) cc_final: 0.8469 (mmmm) REVERT: B 123 MET cc_start: 0.9302 (mtp) cc_final: 0.9035 (ttm) REVERT: B 133 LYS cc_start: 0.8647 (tptp) cc_final: 0.8342 (ptmt) REVERT: C 14 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7772 (mtpp) REVERT: C 85 SER cc_start: 0.8963 (m) cc_final: 0.8689 (p) REVERT: C 89 CYS cc_start: 0.7868 (m) cc_final: 0.7582 (m) REVERT: C 94 GLN cc_start: 0.7659 (mt0) cc_final: 0.7194 (tp40) REVERT: C 95 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8017 (mp0) REVERT: C 106 ASN cc_start: 0.8447 (t0) cc_final: 0.8053 (t0) REVERT: C 195 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7405 (tt0) REVERT: C 237 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8160 (ttpp) REVERT: C 259 ILE cc_start: 0.8000 (mp) cc_final: 0.7677 (mt) REVERT: D 70 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7141 (mpt-90) REVERT: D 115 ASP cc_start: 0.8285 (t0) cc_final: 0.8020 (t70) REVERT: D 202 ASN cc_start: 0.8274 (m-40) cc_final: 0.8018 (t0) REVERT: E 43 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7589 (mt-10) REVERT: E 63 ASP cc_start: 0.8700 (p0) cc_final: 0.8406 (p0) REVERT: E 86 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7569 (tp30) REVERT: E 118 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9109 (mt) REVERT: E 124 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: E 146 TRP cc_start: 0.7662 (t-100) cc_final: 0.7243 (t-100) REVERT: E 200 HIS cc_start: 0.8023 (t-170) cc_final: 0.7559 (t70) REVERT: E 237 PHE cc_start: 0.8095 (m-80) cc_final: 0.7566 (m-80) REVERT: F 23 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8283 (p) REVERT: F 36 ASP cc_start: 0.8624 (t0) cc_final: 0.8404 (t0) REVERT: F 86 THR cc_start: 0.8909 (p) cc_final: 0.8600 (m) REVERT: F 163 TYR cc_start: 0.8305 (t80) cc_final: 0.7812 (t80) REVERT: F 183 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: F 220 LYS cc_start: 0.8528 (pttt) cc_final: 0.7924 (ttpt) REVERT: F 275 LEU cc_start: 0.8854 (mt) cc_final: 0.8482 (tt) REVERT: F 290 TRP cc_start: 0.8858 (m100) cc_final: 0.8455 (m100) REVERT: F 297 TYR cc_start: 0.7822 (m-80) cc_final: 0.7354 (m-80) REVERT: F 319 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8754 (mmt180) REVERT: F 327 ASP cc_start: 0.6978 (t0) cc_final: 0.6431 (p0) REVERT: F 385 LEU cc_start: 0.8436 (mm) cc_final: 0.8112 (mm) outliers start: 155 outliers final: 125 residues processed: 522 average time/residue: 0.2918 time to fit residues: 227.5832 Evaluate side-chains 553 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 422 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 221 HIS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17379 Z= 0.225 Angle : 0.701 15.179 23615 Z= 0.354 Chirality : 0.047 0.271 2571 Planarity : 0.006 0.076 2941 Dihedral : 11.993 86.864 2703 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.66 % Favored : 88.19 % Rotamer: Outliers : 6.25 % Allowed : 28.10 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.71 (0.18), residues: 2049 helix: -0.49 (0.19), residues: 748 sheet: -2.36 (0.34), residues: 217 loop : -2.72 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 152 HIS 0.007 0.001 HIS A 60 PHE 0.023 0.002 PHE D 238 TYR 0.026 0.002 TYR B 169 ARG 0.008 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 473 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6752 (mtt) cc_final: 0.6523 (mmm) REVERT: A 74 ARG cc_start: 0.7150 (tpm170) cc_final: 0.6928 (tpm170) REVERT: A 99 GLU cc_start: 0.8848 (tp30) cc_final: 0.8347 (tp30) REVERT: A 114 GLN cc_start: 0.8044 (pt0) cc_final: 0.7418 (mp10) REVERT: A 121 SER cc_start: 0.9075 (t) cc_final: 0.8496 (m) REVERT: A 152 GLN cc_start: 0.8172 (pt0) cc_final: 0.7251 (tp40) REVERT: A 181 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8504 (ptmm) REVERT: A 192 GLU cc_start: 0.8483 (tt0) cc_final: 0.8232 (pm20) REVERT: A 237 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 253 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8787 (mmmt) REVERT: A 272 ASP cc_start: 0.8458 (t0) cc_final: 0.8052 (t70) REVERT: A 276 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 287 ASN cc_start: 0.9161 (m110) cc_final: 0.8649 (m-40) REVERT: A 299 ILE cc_start: 0.9180 (mt) cc_final: 0.8925 (mp) REVERT: A 313 ILE cc_start: 0.9500 (mt) cc_final: 0.9140 (mm) REVERT: A 342 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 359 LEU cc_start: 0.9185 (tp) cc_final: 0.8151 (tp) REVERT: A 435 THR cc_start: 0.8827 (t) cc_final: 0.8096 (p) REVERT: A 439 ASP cc_start: 0.7908 (m-30) cc_final: 0.7383 (m-30) REVERT: A 464 GLN cc_start: 0.8583 (mp10) cc_final: 0.7855 (mp10) REVERT: A 490 TYR cc_start: 0.7851 (t80) cc_final: 0.7200 (t80) REVERT: A 513 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8118 (ttm-80) REVERT: A 601 GLU cc_start: 0.8192 (tt0) cc_final: 0.7983 (tt0) REVERT: A 629 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6469 (mt-10) REVERT: A 638 ASP cc_start: 0.8364 (m-30) cc_final: 0.7934 (t0) REVERT: A 707 TRP cc_start: 0.8467 (m100) cc_final: 0.8043 (m100) REVERT: A 715 LEU cc_start: 0.9034 (mt) cc_final: 0.8704 (mt) REVERT: A 718 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7993 (ttp-170) REVERT: A 724 ARG cc_start: 0.8595 (mtp180) cc_final: 0.7371 (mmp-170) REVERT: A 725 TRP cc_start: 0.9133 (p-90) cc_final: 0.7547 (p-90) REVERT: B 96 ARG cc_start: 0.7714 (ttm110) cc_final: 0.6726 (tpp80) REVERT: B 97 LYS cc_start: 0.8696 (tptp) cc_final: 0.8390 (mttm) REVERT: B 122 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8409 (mmmm) REVERT: B 123 MET cc_start: 0.9231 (mtp) cc_final: 0.9018 (ttm) REVERT: B 133 LYS cc_start: 0.8657 (tptp) cc_final: 0.8332 (ptmt) REVERT: C 14 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7637 (mtpp) REVERT: C 85 SER cc_start: 0.8919 (m) cc_final: 0.8634 (p) REVERT: C 89 CYS cc_start: 0.7835 (m) cc_final: 0.7557 (m) REVERT: C 94 GLN cc_start: 0.7648 (mt0) cc_final: 0.7180 (tp40) REVERT: C 95 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7713 (mp0) REVERT: C 106 ASN cc_start: 0.8311 (t0) cc_final: 0.7870 (t0) REVERT: C 133 LYS cc_start: 0.8598 (tptt) cc_final: 0.8104 (pttp) REVERT: C 195 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7586 (tt0) REVERT: C 237 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8156 (ttpp) REVERT: C 259 ILE cc_start: 0.7979 (mp) cc_final: 0.7616 (mt) REVERT: D 70 ARG cc_start: 0.7554 (mmm160) cc_final: 0.7105 (mpt-90) REVERT: D 115 ASP cc_start: 0.8187 (t0) cc_final: 0.7951 (t70) REVERT: D 180 PRO cc_start: 0.9186 (Cg_endo) cc_final: 0.8907 (Cg_exo) REVERT: E 43 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7492 (mt-10) REVERT: E 63 ASP cc_start: 0.8580 (p0) cc_final: 0.8309 (p0) REVERT: E 86 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7415 (tp30) REVERT: E 118 ILE cc_start: 0.9405 (tp) cc_final: 0.9083 (mt) REVERT: E 124 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: E 146 TRP cc_start: 0.7649 (t-100) cc_final: 0.7199 (t-100) REVERT: E 200 HIS cc_start: 0.7777 (t-170) cc_final: 0.7398 (t70) REVERT: F 23 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8195 (p) REVERT: F 36 ASP cc_start: 0.8582 (t0) cc_final: 0.8357 (t0) REVERT: F 45 MET cc_start: 0.6088 (mmm) cc_final: 0.5402 (mtm) REVERT: F 86 THR cc_start: 0.9048 (p) cc_final: 0.8771 (m) REVERT: F 131 LYS cc_start: 0.8351 (tttp) cc_final: 0.7626 (tppt) REVERT: F 183 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7460 (pp20) REVERT: F 220 LYS cc_start: 0.8536 (pttt) cc_final: 0.7954 (ttpt) REVERT: F 275 LEU cc_start: 0.8789 (mt) cc_final: 0.8487 (tt) REVERT: F 290 TRP cc_start: 0.8801 (m100) cc_final: 0.8437 (m100) REVERT: F 297 TYR cc_start: 0.7672 (m-80) cc_final: 0.7125 (m-80) REVERT: F 319 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8748 (mmt180) REVERT: F 327 ASP cc_start: 0.6908 (t0) cc_final: 0.6424 (p0) REVERT: F 385 LEU cc_start: 0.8337 (mm) cc_final: 0.8054 (mm) outliers start: 107 outliers final: 86 residues processed: 532 average time/residue: 0.2841 time to fit residues: 225.9246 Evaluate side-chains 530 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 440 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 TYR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17379 Z= 0.228 Angle : 0.700 14.213 23615 Z= 0.353 Chirality : 0.047 0.260 2571 Planarity : 0.006 0.070 2941 Dihedral : 11.809 89.325 2702 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.01 % Favored : 87.85 % Rotamer: Outliers : 6.83 % Allowed : 28.39 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.59 (0.18), residues: 2049 helix: -0.34 (0.19), residues: 745 sheet: -2.25 (0.35), residues: 211 loop : -2.70 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 272 HIS 0.008 0.001 HIS A 60 PHE 0.041 0.002 PHE E 116 TYR 0.032 0.002 TYR F 303 ARG 0.013 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 463 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.6664 (mtt) cc_final: 0.6404 (mmm) REVERT: A 71 MET cc_start: 0.8171 (tpt) cc_final: 0.7794 (tpt) REVERT: A 99 GLU cc_start: 0.8862 (tp30) cc_final: 0.8401 (tp30) REVERT: A 114 GLN cc_start: 0.8038 (pt0) cc_final: 0.7497 (mp10) REVERT: A 121 SER cc_start: 0.8966 (t) cc_final: 0.8334 (m) REVERT: A 152 GLN cc_start: 0.8177 (pt0) cc_final: 0.7314 (tp40) REVERT: A 166 SER cc_start: 0.8319 (m) cc_final: 0.7953 (p) REVERT: A 180 GLU cc_start: 0.8766 (tt0) cc_final: 0.8547 (tt0) REVERT: A 181 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8452 (ptmm) REVERT: A 192 GLU cc_start: 0.8472 (tt0) cc_final: 0.8223 (pm20) REVERT: A 194 ASN cc_start: 0.8273 (t0) cc_final: 0.7998 (t0) REVERT: A 237 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 245 ASP cc_start: 0.8716 (m-30) cc_final: 0.7982 (t0) REVERT: A 272 ASP cc_start: 0.8409 (t0) cc_final: 0.7848 (t0) REVERT: A 276 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: A 287 ASN cc_start: 0.9187 (m110) cc_final: 0.8773 (m-40) REVERT: A 299 ILE cc_start: 0.9172 (mt) cc_final: 0.8938 (mp) REVERT: A 313 ILE cc_start: 0.9513 (mt) cc_final: 0.9119 (mm) REVERT: A 342 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8289 (mp0) REVERT: A 359 LEU cc_start: 0.9176 (tp) cc_final: 0.8150 (tp) REVERT: A 435 THR cc_start: 0.8782 (t) cc_final: 0.8063 (p) REVERT: A 439 ASP cc_start: 0.7926 (m-30) cc_final: 0.7442 (m-30) REVERT: A 454 TYR cc_start: 0.7883 (t80) cc_final: 0.7579 (t80) REVERT: A 464 GLN cc_start: 0.8573 (mp10) cc_final: 0.7901 (mp10) REVERT: A 490 TYR cc_start: 0.7919 (t80) cc_final: 0.7339 (t80) REVERT: A 513 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8156 (ttm-80) REVERT: A 550 LYS cc_start: 0.8126 (mttm) cc_final: 0.7902 (mttm) REVERT: A 558 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 577 GLU cc_start: 0.7004 (tt0) cc_final: 0.6751 (tt0) REVERT: A 600 PHE cc_start: 0.8896 (t80) cc_final: 0.8125 (t80) REVERT: A 601 GLU cc_start: 0.8168 (tt0) cc_final: 0.7962 (tt0) REVERT: A 629 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6647 (mt-10) REVERT: A 638 ASP cc_start: 0.8323 (m-30) cc_final: 0.7936 (t0) REVERT: A 707 TRP cc_start: 0.8479 (m100) cc_final: 0.8182 (m100) REVERT: A 718 ARG cc_start: 0.8304 (ttm170) cc_final: 0.8003 (ttp-170) REVERT: A 724 ARG cc_start: 0.8584 (mtp180) cc_final: 0.7339 (mmp-170) REVERT: A 725 TRP cc_start: 0.9137 (p-90) cc_final: 0.7585 (p-90) REVERT: B 96 ARG cc_start: 0.7635 (ttm110) cc_final: 0.6957 (ttm-80) REVERT: B 97 LYS cc_start: 0.8706 (tptp) cc_final: 0.8392 (mttm) REVERT: B 133 LYS cc_start: 0.8631 (tptp) cc_final: 0.8288 (ptmt) REVERT: C 14 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7601 (mtpp) REVERT: C 85 SER cc_start: 0.8911 (m) cc_final: 0.8642 (p) REVERT: C 89 CYS cc_start: 0.7753 (m) cc_final: 0.6097 (m) REVERT: C 94 GLN cc_start: 0.7680 (mt0) cc_final: 0.7108 (tp40) REVERT: C 95 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7675 (mp0) REVERT: C 106 ASN cc_start: 0.8278 (t0) cc_final: 0.7840 (t0) REVERT: C 109 TRP cc_start: 0.8297 (m100) cc_final: 0.6992 (m-10) REVERT: C 133 LYS cc_start: 0.8630 (tptt) cc_final: 0.8116 (pttp) REVERT: C 195 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7521 (tt0) REVERT: C 237 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8184 (ttpp) REVERT: C 259 ILE cc_start: 0.7981 (mp) cc_final: 0.7676 (mt) REVERT: D 70 ARG cc_start: 0.7595 (mmm160) cc_final: 0.7174 (mpt-90) REVERT: D 115 ASP cc_start: 0.8166 (t0) cc_final: 0.7944 (t70) REVERT: D 180 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8900 (Cg_exo) REVERT: E 20 ARG cc_start: 0.8683 (mmp80) cc_final: 0.8407 (mmp80) REVERT: E 43 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7485 (mt-10) REVERT: E 63 ASP cc_start: 0.8540 (p0) cc_final: 0.8231 (p0) REVERT: E 86 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7398 (tp30) REVERT: E 118 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9062 (mt) REVERT: E 146 TRP cc_start: 0.7643 (t-100) cc_final: 0.7227 (t-100) REVERT: E 200 HIS cc_start: 0.7707 (t-170) cc_final: 0.7371 (t70) REVERT: F 23 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8138 (p) REVERT: F 36 ASP cc_start: 0.8592 (t0) cc_final: 0.8355 (t0) REVERT: F 45 MET cc_start: 0.6387 (mmm) cc_final: 0.5714 (mtm) REVERT: F 86 THR cc_start: 0.9041 (p) cc_final: 0.8776 (m) REVERT: F 131 LYS cc_start: 0.8334 (tttp) cc_final: 0.7574 (tppt) REVERT: F 183 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7480 (pp20) REVERT: F 189 MET cc_start: 0.7632 (tpp) cc_final: 0.7403 (tpp) REVERT: F 220 LYS cc_start: 0.8541 (pttt) cc_final: 0.7961 (ttpt) REVERT: F 275 LEU cc_start: 0.8794 (mt) cc_final: 0.8519 (tt) REVERT: F 290 TRP cc_start: 0.8808 (m100) cc_final: 0.8425 (m100) REVERT: F 297 TYR cc_start: 0.7668 (m-80) cc_final: 0.6855 (m-80) REVERT: F 319 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8737 (mmt-90) REVERT: F 327 ASP cc_start: 0.6897 (t0) cc_final: 0.6425 (p0) outliers start: 117 outliers final: 88 residues processed: 525 average time/residue: 0.2898 time to fit residues: 226.5183 Evaluate side-chains 539 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 447 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 3.9990 chunk 79 optimal weight: 0.0170 chunk 119 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN D 212 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17379 Z= 0.185 Angle : 0.693 12.796 23615 Z= 0.346 Chirality : 0.046 0.226 2571 Planarity : 0.005 0.070 2941 Dihedral : 11.598 88.956 2702 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 4.73 % Allowed : 30.08 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.52 (0.18), residues: 2049 helix: -0.35 (0.19), residues: 761 sheet: -2.16 (0.36), residues: 204 loop : -2.65 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 152 HIS 0.008 0.001 HIS A 60 PHE 0.030 0.002 PHE E 116 TYR 0.032 0.002 TYR C 250 ARG 0.008 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 492 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8296 (tt0) cc_final: 0.7986 (tt0) REVERT: A 65 MET cc_start: 0.6466 (mtt) cc_final: 0.6226 (mtt) REVERT: A 71 MET cc_start: 0.8141 (tpt) cc_final: 0.7773 (tpt) REVERT: A 99 GLU cc_start: 0.8852 (tp30) cc_final: 0.8368 (tp30) REVERT: A 114 GLN cc_start: 0.8103 (pt0) cc_final: 0.7565 (mp10) REVERT: A 152 GLN cc_start: 0.8127 (pt0) cc_final: 0.7224 (tp40) REVERT: A 166 SER cc_start: 0.8243 (m) cc_final: 0.7870 (p) REVERT: A 171 ARG cc_start: 0.7090 (mtm180) cc_final: 0.6785 (mtp180) REVERT: A 192 GLU cc_start: 0.8328 (tt0) cc_final: 0.8027 (pm20) REVERT: A 237 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 272 ASP cc_start: 0.8189 (t0) cc_final: 0.7762 (t0) REVERT: A 276 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 287 ASN cc_start: 0.9181 (m110) cc_final: 0.8816 (m-40) REVERT: A 313 ILE cc_start: 0.9492 (mt) cc_final: 0.9102 (mm) REVERT: A 334 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 342 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8251 (mp0) REVERT: A 359 LEU cc_start: 0.9101 (tp) cc_final: 0.8024 (tp) REVERT: A 385 ARG cc_start: 0.6601 (mmp-170) cc_final: 0.6365 (mmm160) REVERT: A 435 THR cc_start: 0.8657 (t) cc_final: 0.8240 (p) REVERT: A 439 ASP cc_start: 0.7903 (m-30) cc_final: 0.7591 (m-30) REVERT: A 464 GLN cc_start: 0.8533 (mp10) cc_final: 0.7897 (mp10) REVERT: A 490 TYR cc_start: 0.7703 (t80) cc_final: 0.7187 (t80) REVERT: A 513 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8223 (ttm-80) REVERT: A 558 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 560 LYS cc_start: 0.8532 (mttp) cc_final: 0.8205 (mmmt) REVERT: A 600 PHE cc_start: 0.8731 (t80) cc_final: 0.8289 (t80) REVERT: A 629 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6620 (mt-10) REVERT: A 638 ASP cc_start: 0.8297 (m-30) cc_final: 0.7943 (t0) REVERT: A 707 TRP cc_start: 0.8376 (m100) cc_final: 0.7868 (m100) REVERT: A 718 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8013 (mtp180) REVERT: A 724 ARG cc_start: 0.8540 (mtp180) cc_final: 0.7386 (mmp-170) REVERT: A 725 TRP cc_start: 0.9097 (p-90) cc_final: 0.8292 (p-90) REVERT: B 96 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6265 (tpp-160) REVERT: B 97 LYS cc_start: 0.8667 (tptp) cc_final: 0.8427 (mttp) REVERT: B 122 LYS cc_start: 0.9029 (ptmt) cc_final: 0.8201 (mmmt) REVERT: B 123 MET cc_start: 0.9276 (ttm) cc_final: 0.8952 (mtt) REVERT: B 133 LYS cc_start: 0.8624 (tptp) cc_final: 0.8331 (ptpt) REVERT: C 14 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7629 (mtpp) REVERT: C 63 PHE cc_start: 0.8640 (t80) cc_final: 0.8425 (t80) REVERT: C 85 SER cc_start: 0.8810 (m) cc_final: 0.8536 (p) REVERT: C 89 CYS cc_start: 0.7602 (m) cc_final: 0.7388 (m) REVERT: C 94 GLN cc_start: 0.7619 (mt0) cc_final: 0.7139 (tp40) REVERT: C 106 ASN cc_start: 0.8020 (t0) cc_final: 0.7569 (t0) REVERT: C 133 LYS cc_start: 0.8682 (tptt) cc_final: 0.8197 (pttp) REVERT: C 156 TRP cc_start: 0.8046 (t60) cc_final: 0.7816 (t60) REVERT: C 195 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7523 (tt0) REVERT: C 237 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8238 (ttpp) REVERT: C 259 ILE cc_start: 0.8031 (mp) cc_final: 0.6762 (mt) REVERT: D 70 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7195 (mpt-90) REVERT: D 110 ILE cc_start: 0.8005 (pt) cc_final: 0.7691 (tp) REVERT: D 115 ASP cc_start: 0.8078 (t0) cc_final: 0.7817 (t70) REVERT: D 180 PRO cc_start: 0.9153 (Cg_endo) cc_final: 0.8917 (Cg_exo) REVERT: E 43 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7416 (mt-10) REVERT: E 71 LEU cc_start: 0.8390 (tp) cc_final: 0.8095 (tp) REVERT: E 86 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7394 (tp30) REVERT: E 118 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9023 (mt) REVERT: E 202 MET cc_start: 0.8245 (mmm) cc_final: 0.7859 (tpp) REVERT: F 23 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7941 (p) REVERT: F 26 TYR cc_start: 0.7634 (t80) cc_final: 0.7078 (t80) REVERT: F 36 ASP cc_start: 0.8591 (t0) cc_final: 0.8371 (t0) REVERT: F 45 MET cc_start: 0.6455 (mmm) cc_final: 0.5947 (mtm) REVERT: F 82 TYR cc_start: 0.5603 (m-80) cc_final: 0.5284 (m-80) REVERT: F 86 THR cc_start: 0.9041 (p) cc_final: 0.8774 (m) REVERT: F 131 LYS cc_start: 0.8277 (tttp) cc_final: 0.7526 (tppt) REVERT: F 183 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7513 (pp20) REVERT: F 206 MET cc_start: 0.8340 (mmm) cc_final: 0.7833 (tpt) REVERT: F 211 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6772 (p) REVERT: F 220 LYS cc_start: 0.8517 (pttt) cc_final: 0.7933 (ttpt) REVERT: F 290 TRP cc_start: 0.8784 (m100) cc_final: 0.8414 (m100) REVERT: F 297 TYR cc_start: 0.7741 (m-80) cc_final: 0.6826 (m-80) REVERT: F 301 MET cc_start: 0.8199 (ppp) cc_final: 0.7971 (ppp) REVERT: F 319 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8753 (mmt180) REVERT: F 327 ASP cc_start: 0.7058 (t0) cc_final: 0.6549 (p0) REVERT: F 390 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8274 (Cg_endo) outliers start: 81 outliers final: 64 residues processed: 537 average time/residue: 0.2971 time to fit residues: 236.9127 Evaluate side-chains 521 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 452 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 185 optimal weight: 0.0010 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.0670 chunk 57 optimal weight: 9.9990 chunk 168 optimal weight: 0.0970 chunk 175 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.6326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17379 Z= 0.215 Angle : 0.699 12.818 23615 Z= 0.351 Chirality : 0.048 0.289 2571 Planarity : 0.005 0.075 2941 Dihedral : 11.466 86.275 2702 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.98 % Favored : 88.92 % Rotamer: Outliers : 4.85 % Allowed : 30.84 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.41 (0.18), residues: 2049 helix: -0.26 (0.19), residues: 759 sheet: -1.83 (0.37), residues: 193 loop : -2.63 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 272 HIS 0.011 0.001 HIS C 205 PHE 0.030 0.002 PHE E 116 TYR 0.036 0.002 TYR F 303 ARG 0.008 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 460 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8322 (tt0) cc_final: 0.8023 (tt0) REVERT: A 65 MET cc_start: 0.6499 (mtt) cc_final: 0.6230 (mmm) REVERT: A 71 MET cc_start: 0.8073 (tpt) cc_final: 0.7708 (tpt) REVERT: A 99 GLU cc_start: 0.8849 (tp30) cc_final: 0.8467 (tp30) REVERT: A 114 GLN cc_start: 0.8222 (pt0) cc_final: 0.7560 (mp10) REVERT: A 152 GLN cc_start: 0.8080 (pt0) cc_final: 0.7212 (tp40) REVERT: A 166 SER cc_start: 0.8295 (m) cc_final: 0.7916 (p) REVERT: A 169 LYS cc_start: 0.7148 (mtpp) cc_final: 0.6470 (mtmm) REVERT: A 192 GLU cc_start: 0.8359 (tt0) cc_final: 0.8065 (pm20) REVERT: A 199 TYR cc_start: 0.8910 (t80) cc_final: 0.8397 (t80) REVERT: A 237 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 272 ASP cc_start: 0.8223 (t0) cc_final: 0.7795 (t0) REVERT: A 276 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: A 287 ASN cc_start: 0.9186 (m110) cc_final: 0.8775 (m-40) REVERT: A 334 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 342 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8280 (mp0) REVERT: A 359 LEU cc_start: 0.9119 (tp) cc_final: 0.8050 (tp) REVERT: A 385 ARG cc_start: 0.6644 (mmp-170) cc_final: 0.6382 (mmm160) REVERT: A 435 THR cc_start: 0.8638 (t) cc_final: 0.8079 (p) REVERT: A 439 ASP cc_start: 0.7924 (m-30) cc_final: 0.7577 (m-30) REVERT: A 464 GLN cc_start: 0.8536 (mp10) cc_final: 0.7887 (mp10) REVERT: A 490 TYR cc_start: 0.7741 (t80) cc_final: 0.7235 (t80) REVERT: A 513 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8235 (ttm-80) REVERT: A 558 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 600 PHE cc_start: 0.8786 (t80) cc_final: 0.8421 (t80) REVERT: A 629 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6674 (mt-10) REVERT: A 638 ASP cc_start: 0.8307 (m-30) cc_final: 0.7936 (t0) REVERT: A 707 TRP cc_start: 0.8385 (m100) cc_final: 0.8068 (m100) REVERT: A 718 ARG cc_start: 0.8271 (ttm170) cc_final: 0.8009 (mtp180) REVERT: A 724 ARG cc_start: 0.8501 (mtp180) cc_final: 0.7358 (mmp-170) REVERT: A 725 TRP cc_start: 0.9099 (p-90) cc_final: 0.7661 (p-90) REVERT: B 96 ARG cc_start: 0.7429 (ttm110) cc_final: 0.6243 (tpp80) REVERT: B 97 LYS cc_start: 0.8676 (tptp) cc_final: 0.8367 (mttm) REVERT: B 107 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 123 MET cc_start: 0.9288 (ttm) cc_final: 0.9076 (mtt) REVERT: B 129 TYR cc_start: 0.8635 (t80) cc_final: 0.8392 (t80) REVERT: B 133 LYS cc_start: 0.8617 (tptp) cc_final: 0.8217 (ptmt) REVERT: C 14 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7708 (mtpp) REVERT: C 85 SER cc_start: 0.8798 (m) cc_final: 0.8552 (p) REVERT: C 89 CYS cc_start: 0.7647 (m) cc_final: 0.7404 (m) REVERT: C 94 GLN cc_start: 0.7750 (mt0) cc_final: 0.7202 (tp40) REVERT: C 106 ASN cc_start: 0.8070 (t0) cc_final: 0.7632 (t0) REVERT: C 133 LYS cc_start: 0.8725 (tptt) cc_final: 0.8235 (pttp) REVERT: C 156 TRP cc_start: 0.8065 (t60) cc_final: 0.7851 (t60) REVERT: C 195 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7566 (tt0) REVERT: C 212 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8626 (t0) REVERT: C 237 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8199 (ttpp) REVERT: D 70 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7275 (mpt-90) REVERT: D 115 ASP cc_start: 0.8098 (t0) cc_final: 0.7840 (t70) REVERT: D 180 PRO cc_start: 0.9171 (Cg_endo) cc_final: 0.8949 (Cg_exo) REVERT: E 43 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7382 (mt-10) REVERT: E 86 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7399 (tp30) REVERT: E 89 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7694 (tmt-80) REVERT: E 118 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8985 (mt) REVERT: E 262 ARG cc_start: 0.7193 (ttm170) cc_final: 0.6885 (mtt180) REVERT: F 23 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7975 (p) REVERT: F 36 ASP cc_start: 0.8579 (t0) cc_final: 0.8326 (t0) REVERT: F 45 MET cc_start: 0.6576 (mmm) cc_final: 0.6093 (mtm) REVERT: F 82 TYR cc_start: 0.5591 (m-80) cc_final: 0.5275 (m-80) REVERT: F 86 THR cc_start: 0.9080 (p) cc_final: 0.8794 (m) REVERT: F 98 MET cc_start: 0.5349 (mmt) cc_final: 0.4934 (mpp) REVERT: F 131 LYS cc_start: 0.8318 (tttp) cc_final: 0.7556 (tppt) REVERT: F 202 LYS cc_start: 0.7814 (mptt) cc_final: 0.7508 (mmtm) REVERT: F 206 MET cc_start: 0.8313 (mmm) cc_final: 0.8004 (tpt) REVERT: F 220 LYS cc_start: 0.8587 (pttt) cc_final: 0.7933 (ttpt) REVERT: F 261 ARG cc_start: 0.6018 (ttp-170) cc_final: 0.5738 (ttm170) REVERT: F 290 TRP cc_start: 0.8765 (m100) cc_final: 0.8374 (m100) REVERT: F 297 TYR cc_start: 0.7773 (m-80) cc_final: 0.6876 (m-80) REVERT: F 301 MET cc_start: 0.8164 (ppp) cc_final: 0.7913 (ppp) REVERT: F 319 ARG cc_start: 0.9109 (ttp80) cc_final: 0.8774 (mmt180) REVERT: F 327 ASP cc_start: 0.7059 (t0) cc_final: 0.6573 (p0) REVERT: F 390 PRO cc_start: 0.8441 (Cg_exo) cc_final: 0.8214 (Cg_endo) outliers start: 83 outliers final: 68 residues processed: 509 average time/residue: 0.2826 time to fit residues: 216.2345 Evaluate side-chains 514 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 440 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 331 HIS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 3.9990 chunk 119 optimal weight: 0.0030 chunk 93 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 179 HIS D 212 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17379 Z= 0.186 Angle : 0.701 13.073 23615 Z= 0.348 Chirality : 0.047 0.235 2571 Planarity : 0.005 0.066 2941 Dihedral : 11.336 82.313 2702 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.44 % Favored : 89.51 % Rotamer: Outliers : 3.86 % Allowed : 31.19 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.37 (0.18), residues: 2049 helix: -0.24 (0.19), residues: 750 sheet: -1.93 (0.36), residues: 200 loop : -2.56 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 272 HIS 0.018 0.001 HIS C 205 PHE 0.027 0.002 PHE E 116 TYR 0.035 0.002 TYR C 250 ARG 0.009 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 485 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8360 (tt0) cc_final: 0.8119 (tt0) REVERT: A 65 MET cc_start: 0.6371 (mtt) cc_final: 0.6092 (mtt) REVERT: A 99 GLU cc_start: 0.8779 (tp30) cc_final: 0.8161 (tp30) REVERT: A 101 ASP cc_start: 0.8342 (t70) cc_final: 0.7976 (t0) REVERT: A 103 LEU cc_start: 0.9159 (mt) cc_final: 0.8749 (mm) REVERT: A 114 GLN cc_start: 0.8186 (pt0) cc_final: 0.7550 (mp10) REVERT: A 138 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8246 (mtpt) REVERT: A 166 SER cc_start: 0.8237 (m) cc_final: 0.7855 (p) REVERT: A 169 LYS cc_start: 0.7095 (mtpp) cc_final: 0.6409 (mtmm) REVERT: A 192 GLU cc_start: 0.8303 (tt0) cc_final: 0.7908 (pm20) REVERT: A 194 ASN cc_start: 0.8121 (t0) cc_final: 0.7729 (t0) REVERT: A 196 ILE cc_start: 0.9015 (mp) cc_final: 0.8669 (mm) REVERT: A 199 TYR cc_start: 0.8943 (t80) cc_final: 0.8372 (t80) REVERT: A 237 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7147 (mt-10) REVERT: A 257 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7548 (mmtm) REVERT: A 272 ASP cc_start: 0.8095 (t0) cc_final: 0.7746 (t0) REVERT: A 276 GLU cc_start: 0.8498 (tp30) cc_final: 0.8049 (tm-30) REVERT: A 287 ASN cc_start: 0.9179 (m110) cc_final: 0.8771 (m-40) REVERT: A 334 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 342 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8255 (mp0) REVERT: A 359 LEU cc_start: 0.9123 (tp) cc_final: 0.8210 (tp) REVERT: A 385 ARG cc_start: 0.6559 (mmp-170) cc_final: 0.6339 (mmm160) REVERT: A 403 PRO cc_start: 0.8026 (Cg_endo) cc_final: 0.7677 (Cg_exo) REVERT: A 435 THR cc_start: 0.8589 (t) cc_final: 0.8175 (p) REVERT: A 464 GLN cc_start: 0.8528 (mp10) cc_final: 0.7863 (mp10) REVERT: A 490 TYR cc_start: 0.7655 (t80) cc_final: 0.7235 (t80) REVERT: A 513 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8161 (ttm-80) REVERT: A 537 LYS cc_start: 0.9029 (mttm) cc_final: 0.8817 (mtpt) REVERT: A 558 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 600 PHE cc_start: 0.8637 (t80) cc_final: 0.8057 (t80) REVERT: A 629 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6406 (mt-10) REVERT: A 638 ASP cc_start: 0.8308 (m-30) cc_final: 0.8071 (t0) REVERT: A 718 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7973 (mtp180) REVERT: A 724 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7341 (mmp-170) REVERT: A 725 TRP cc_start: 0.9064 (p-90) cc_final: 0.7645 (p-90) REVERT: A 748 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 97 LYS cc_start: 0.8645 (tptp) cc_final: 0.8352 (mttm) REVERT: B 107 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 133 LYS cc_start: 0.8640 (tptp) cc_final: 0.8317 (ptpt) REVERT: B 178 TYR cc_start: 0.8524 (m-80) cc_final: 0.8059 (m-80) REVERT: C 14 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7569 (mtpp) REVERT: C 85 SER cc_start: 0.8734 (m) cc_final: 0.8491 (p) REVERT: C 94 GLN cc_start: 0.7628 (mt0) cc_final: 0.7282 (tp40) REVERT: C 106 ASN cc_start: 0.8018 (t0) cc_final: 0.7582 (t0) REVERT: C 133 LYS cc_start: 0.8710 (tptt) cc_final: 0.8175 (ptpp) REVERT: C 156 TRP cc_start: 0.8042 (t60) cc_final: 0.7828 (t60) REVERT: C 195 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7482 (tt0) REVERT: C 237 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8257 (ttpp) REVERT: D 70 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7212 (mpt-90) REVERT: D 115 ASP cc_start: 0.7993 (t0) cc_final: 0.7770 (t70) REVERT: D 205 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8309 (t70) REVERT: E 43 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7356 (mt-10) REVERT: E 86 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7183 (tp30) REVERT: E 89 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7719 (tpt170) REVERT: E 118 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8953 (mt) REVERT: E 200 HIS cc_start: 0.7346 (t70) cc_final: 0.6899 (t-170) REVERT: F 23 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8040 (p) REVERT: F 26 TYR cc_start: 0.7722 (t80) cc_final: 0.7212 (t80) REVERT: F 36 ASP cc_start: 0.8569 (t0) cc_final: 0.8324 (t0) REVERT: F 82 TYR cc_start: 0.5548 (m-80) cc_final: 0.5283 (m-80) REVERT: F 86 THR cc_start: 0.9036 (p) cc_final: 0.8763 (m) REVERT: F 98 MET cc_start: 0.5329 (mmt) cc_final: 0.4775 (mpp) REVERT: F 187 PHE cc_start: 0.8959 (m-80) cc_final: 0.8494 (t80) REVERT: F 220 LYS cc_start: 0.8511 (pttt) cc_final: 0.8013 (ttpt) REVERT: F 244 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7063 (tm-30) REVERT: F 290 TRP cc_start: 0.8756 (m100) cc_final: 0.8344 (m100) REVERT: F 297 TYR cc_start: 0.7733 (m-80) cc_final: 0.6761 (m-80) REVERT: F 327 ASP cc_start: 0.7068 (t0) cc_final: 0.6551 (p0) REVERT: F 390 PRO cc_start: 0.8377 (Cg_exo) cc_final: 0.8162 (Cg_endo) outliers start: 66 outliers final: 51 residues processed: 526 average time/residue: 0.2843 time to fit residues: 222.9232 Evaluate side-chains 510 residues out of total 1762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 453 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 5 PHE Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 206 TRP Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 TYR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 151 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 164 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 179 HIS C 22 HIS C 205 HIS D 183 ASN ** D 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.146335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121262 restraints weight = 33134.359| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.11 r_work: 0.3492 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17379 Z= 0.217 Angle : 0.710 13.030 23615 Z= 0.355 Chirality : 0.047 0.218 2571 Planarity : 0.005 0.066 2941 Dihedral : 11.246 81.919 2702 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.88 % Favored : 89.02 % Rotamer: Outliers : 3.56 % Allowed : 32.36 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.18), residues: 2049 helix: -0.12 (0.19), residues: 755 sheet: -1.86 (0.37), residues: 200 loop : -2.50 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 272 HIS 0.008 0.001 HIS F 226 PHE 0.028 0.002 PHE A 482 TYR 0.035 0.002 TYR F 303 ARG 0.009 0.000 ARG F 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.35 seconds wall clock time: 82 minutes 37.81 seconds (4957.81 seconds total)