Starting phenix.real_space_refine on Sat Sep 28 01:46:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/09_2024/6o7h_0641.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 50 5.49 5 S 49 5.16 5 C 11014 2.51 5 N 3083 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6152 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1047 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2265 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "F" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2223 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 93, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3079 SG CYS A 389 57.900 85.339 89.908 1.00 26.12 S ATOM 3099 SG CYS A 392 53.925 83.414 90.176 1.00 20.38 S ATOM 3254 SG CYS A 413 55.553 86.020 92.716 1.00 30.17 S ATOM 3274 SG CYS A 416 56.496 82.553 92.693 1.00 30.70 S ATOM 8026 SG CYS C 113 73.888 99.035 65.322 1.00 24.94 S ATOM 8093 SG CYS C 122 74.316 98.299 61.726 1.00 18.20 S ATOM 8113 SG CYS C 125 71.610 95.804 64.201 1.00 17.21 S ATOM 10291 SG CYS D 113 93.830 71.709 67.401 1.00 32.50 S ATOM 10358 SG CYS D 122 96.213 71.721 64.605 1.00 31.10 S ATOM 10378 SG CYS D 125 91.608 70.721 64.658 1.00 23.12 S Time building chain proxies: 10.38, per 1000 atoms: 0.59 Number of scatterers: 17576 At special positions: 0 Unit cell: (127.413, 119.79, 150.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 49 16.00 P 50 15.00 O 3377 8.00 N 3083 7.00 C 11014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied TRANS " UNK F 40 " - " ARG F 39 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 29 sheets defined 42.3% alpha, 15.8% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.557A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.893A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.778A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.591A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.764A pdb=" N PHE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.507A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 171 through 184 Proline residue: A 177 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 282 removed outlier: 3.557A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.572A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.733A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.854A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.663A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.664A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.737A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.877A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.897A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.839A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 4.526A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.355A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.309A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.835A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.203A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.555A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.861A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 3.616A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 4.019A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.787A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.609A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.967A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.509A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.919A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.585A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.617A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.799A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.641A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 247 through 254 removed outlier: 4.032A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.905A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.865A pdb=" N GLU D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'E' and resid 20 through 36 Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.888A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.919A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 removed outlier: 3.569A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.845A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.554A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.755A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.591A pdb=" N UNK F 46 " --> pdb=" O UNK F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 4.304A pdb=" N UNK F 58 " --> pdb=" O UNK F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 132 removed outlier: 3.572A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.815A pdb=" N UNK F 141 " --> pdb=" O UNK F 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK F 142 " --> pdb=" O UNK F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 151 through 155 removed outlier: 4.183A pdb=" N UNK F 155 " --> pdb=" O UNK F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 155' Processing helix chain 'F' and resid 160 through 169 removed outlier: 4.251A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK F 169 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.935A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.677A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.564A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.837A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 4.113A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.313A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.224A pdb=" N LEU A 119 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.708A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA5, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 4.265A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 430 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 586 removed outlier: 7.044A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.675A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.887A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.792A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.706A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.726A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.612A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.392A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 169 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 7.294A pdb=" N GLY D 232 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL F 211 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.252A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 134 removed outlier: 3.646A pdb=" N VAL E 127 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 252 through 254 removed outlier: 4.608A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.535A pdb=" N LEU E 230 " --> pdb=" O PHE E 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.565A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.718A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 5.21 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: 4576 1.33 - 1.45: 3643 1.45 - 1.57: 9655 1.57 - 1.69: 97 1.69 - 1.81: 80 Bond restraints: 18051 Sorted by residual: bond pdb=" C5 A K 3 " pdb=" C6 A K 3 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 A K 1 " pdb=" C6 A K 1 " ideal model delta sigma weight residual 1.406 1.328 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 A K 4 " pdb=" C6 A K 4 " ideal model delta sigma weight residual 1.406 1.329 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 1.593 1.649 -0.056 1.50e-02 4.44e+03 1.37e+01 bond pdb=" C5 A K 2 " pdb=" C6 A K 2 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 18046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 24507 4.90 - 9.80: 117 9.80 - 14.70: 7 14.70 - 19.60: 2 19.60 - 24.50: 3 Bond angle restraints: 24636 Sorted by residual: angle pdb=" O3' A K 2 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 104.00 85.62 18.38 1.50e+00 4.44e-01 1.50e+02 angle pdb=" OP2 A K 3 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 108.00 83.50 24.50 3.00e+00 1.11e-01 6.67e+01 angle pdb=" OP1 A K 1 " pdb=" P A K 1 " pdb=" O5' A K 1 " ideal model delta sigma weight residual 108.00 87.41 20.59 3.00e+00 1.11e-01 4.71e+01 angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N PRO B 33 " pdb=" CA PRO B 33 " pdb=" CB PRO B 33 " ideal model delta sigma weight residual 103.25 110.20 -6.95 1.05e+00 9.07e-01 4.38e+01 ... (remaining 24631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 10557 34.35 - 68.70: 242 68.70 - 103.05: 26 103.05 - 137.40: 0 137.40 - 171.74: 3 Dihedral angle restraints: 10828 sinusoidal: 4758 harmonic: 6070 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual -128.00 43.74 -171.74 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 5 " pdb=" C1' C G 5 " pdb=" N1 C G 5 " pdb=" C2 C G 5 " ideal model delta sinusoidal sigma weight residual -128.00 30.12 -158.12 1 1.70e+01 3.46e-03 6.40e+01 dihedral pdb=" C4' A K 2 " pdb=" O4' A K 2 " pdb=" C1' A K 2 " pdb=" C2' A K 2 " ideal model delta sinusoidal sigma weight residual -21.00 26.55 -47.55 1 8.00e+00 1.56e-02 4.88e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2492 0.116 - 0.231: 216 0.231 - 0.347: 13 0.347 - 0.463: 1 0.463 - 0.579: 2 Chirality restraints: 2724 Sorted by residual: chirality pdb=" P A K 1 " pdb=" OP1 A K 1 " pdb=" OP2 A K 1 " pdb=" O5' A K 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" P A K 3 " pdb=" OP1 A K 3 " pdb=" OP2 A K 3 " pdb=" O5' A K 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C1' C G 5 " pdb=" O4' C G 5 " pdb=" C2' C G 5 " pdb=" N1 C G 5 " both_signs ideal model delta sigma weight residual False 2.45 2.10 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 2721 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 252 " 0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C GLY A 252 " -0.091 2.00e-02 2.50e+03 pdb=" O GLY A 252 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 253 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 71 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C MET A 71 " 0.077 2.00e-02 2.50e+03 pdb=" O MET A 71 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE A 72 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA E 47 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.025 2.00e-02 2.50e+03 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 10 2.26 - 2.92: 6851 2.92 - 3.58: 23617 3.58 - 4.24: 42811 4.24 - 4.90: 71232 Nonbonded interactions: 144521 Sorted by model distance: nonbonded pdb=" O3' C H 35 " pdb=" P G H 101 " model vdw 1.596 3.400 nonbonded pdb=" P A K 1 " pdb=" O3' A K 4 " model vdw 1.628 3.400 nonbonded pdb=" O2' A K 1 " pdb=" OP1 A K 2 " model vdw 2.055 3.040 nonbonded pdb=" O5' A K 1 " pdb=" O3' A K 4 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 180 " pdb=" OH TYR A 547 " model vdw 2.204 3.040 ... (remaining 144516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 4 through 26 or resid 34 through 287 or resid 301)) selection = (chain 'D' and (resid 4 through 26 or resid 34 through 287 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 50.130 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.006 0.082 18051 Z= 0.415 Angle : 1.105 24.503 24636 Z= 0.653 Chirality : 0.067 0.579 2724 Planarity : 0.007 0.061 2992 Dihedral : 14.233 171.744 6943 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 1.21 % Allowed : 4.83 % Favored : 93.96 % 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: -4.34 (0.15), residues: 2006 helix: -3.61 (0.12), residues: 771 sheet: -1.91 (0.27), residues: 290 loop : -2.44 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 320 HIS 0.007 0.002 HIS D 22 PHE 0.029 0.003 PHE A 502 TYR 0.029 0.003 TYR C 233 ARG 0.014 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 445 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8305 (mtm) cc_final: 0.7894 (mtt) REVERT: A 158 VAL cc_start: 0.8439 (t) cc_final: 0.8144 (t) REVERT: A 159 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8194 (tppt) REVERT: A 162 TRP cc_start: 0.8459 (t-100) cc_final: 0.8073 (t-100) REVERT: A 167 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7553 (mtmt) REVERT: A 170 LEU cc_start: 0.8991 (tp) cc_final: 0.8659 (tp) REVERT: A 297 MET cc_start: 0.8933 (ttt) cc_final: 0.8664 (ttt) REVERT: A 757 GLU cc_start: 0.7493 (pt0) cc_final: 0.6826 (pt0) outliers start: 20 outliers final: 5 residues processed: 460 average time/residue: 1.5535 time to fit residues: 784.5206 Evaluate side-chains 272 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 267 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 456 GLN A 668 HIS B 72 ASN C 37 ASN C 179 ASN D 22 HIS D 83 ASN D 106 ASN D 179 ASN D 183 ASN F 18 ASN F 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18051 Z= 0.200 Angle : 0.656 15.182 24636 Z= 0.339 Chirality : 0.045 0.220 2724 Planarity : 0.006 0.067 2992 Dihedral : 15.691 178.466 3133 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.84 % Allowed : 16.23 % Favored : 80.93 % 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: -2.88 (0.16), residues: 2006 helix: -1.76 (0.16), residues: 781 sheet: -1.48 (0.28), residues: 278 loop : -2.10 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 131 HIS 0.005 0.001 HIS D 205 PHE 0.014 0.002 PHE B 181 TYR 0.020 0.002 TYR B 125 ARG 0.007 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 296 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8900 (tp) REVERT: A 21 GLN cc_start: 0.7982 (tm130) cc_final: 0.7735 (tm-30) REVERT: A 65 MET cc_start: 0.4857 (ptm) cc_final: 0.4500 (ptm) REVERT: A 71 MET cc_start: 0.8219 (mtm) cc_final: 0.7978 (mtt) REVERT: A 159 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8284 (tppt) REVERT: A 249 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8231 (ttp80) REVERT: A 633 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7342 (mt) REVERT: A 642 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: A 694 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7541 (mtm110) REVERT: A 755 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6934 (mtp85) REVERT: A 757 GLU cc_start: 0.7395 (pt0) cc_final: 0.6974 (pt0) REVERT: B 122 LYS cc_start: 0.7881 (mttt) cc_final: 0.7675 (mttt) REVERT: B 123 MET cc_start: 0.7613 (ttt) cc_final: 0.7354 (ttm) REVERT: D 1 MET cc_start: 0.6983 (tmt) cc_final: 0.6738 (tmt) REVERT: E 176 MET cc_start: 0.8669 (mmm) cc_final: 0.8061 (mmp) REVERT: F 7 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7320 (mmtp) REVERT: F 128 LYS cc_start: 0.6700 (tptt) cc_final: 0.6458 (tttt) REVERT: F 131 LYS cc_start: 0.6676 (mmmm) cc_final: 0.6213 (mtpp) REVERT: F 276 LYS cc_start: 0.5609 (mtpp) cc_final: 0.5295 (mmtm) outliers start: 47 outliers final: 15 residues processed: 321 average time/residue: 1.4439 time to fit residues: 512.1207 Evaluate side-chains 276 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18051 Z= 0.232 Angle : 0.614 14.105 24636 Z= 0.316 Chirality : 0.045 0.208 2724 Planarity : 0.005 0.050 2992 Dihedral : 15.445 177.628 3126 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.98 % Allowed : 17.02 % Favored : 79.00 % 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: -2.05 (0.17), residues: 2006 helix: -0.73 (0.18), residues: 796 sheet: -1.19 (0.28), residues: 302 loop : -1.94 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.006 0.001 HIS D 205 PHE 0.024 0.002 PHE E 15 TYR 0.019 0.002 TYR A 265 ARG 0.012 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 268 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4812 (ptm) cc_final: 0.4464 (ptp) REVERT: A 71 MET cc_start: 0.8123 (mtm) cc_final: 0.7902 (mtt) REVERT: A 155 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: A 158 VAL cc_start: 0.8410 (t) cc_final: 0.8092 (t) REVERT: A 159 LYS cc_start: 0.8776 (tmmt) cc_final: 0.8323 (tppt) REVERT: A 195 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8978 (pt) REVERT: A 513 ARG cc_start: 0.7839 (mpt180) cc_final: 0.7611 (mpt180) REVERT: A 633 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 755 ARG cc_start: 0.7548 (mtp85) cc_final: 0.6967 (mtp85) REVERT: A 757 GLU cc_start: 0.7366 (pt0) cc_final: 0.6912 (pt0) REVERT: A 773 MET cc_start: 0.7987 (mtp) cc_final: 0.7662 (mtp) REVERT: B 123 MET cc_start: 0.7764 (ttt) cc_final: 0.7515 (ttm) REVERT: C 168 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 267 LYS cc_start: 0.8322 (pttm) cc_final: 0.7686 (ptmm) REVERT: D 1 MET cc_start: 0.7051 (tmt) cc_final: 0.6798 (tmt) REVERT: D 185 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7968 (ptp-170) REVERT: E 139 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8267 (mt0) REVERT: E 147 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: E 176 MET cc_start: 0.8765 (mmm) cc_final: 0.8144 (mmp) REVERT: F 131 LYS cc_start: 0.6506 (mmmm) cc_final: 0.6243 (mtpp) REVERT: F 214 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8617 (t) outliers start: 66 outliers final: 15 residues processed: 315 average time/residue: 1.3330 time to fit residues: 467.3231 Evaluate side-chains 272 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 78 optimal weight: 0.0040 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 156 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18051 Z= 0.138 Angle : 0.542 12.598 24636 Z= 0.277 Chirality : 0.042 0.199 2724 Planarity : 0.004 0.048 2992 Dihedral : 15.331 177.857 3125 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.66 % Allowed : 18.47 % Favored : 78.88 % 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: -1.44 (0.18), residues: 2006 helix: -0.01 (0.19), residues: 791 sheet: -1.11 (0.29), residues: 291 loop : -1.72 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 131 HIS 0.003 0.001 HIS F 254 PHE 0.016 0.001 PHE B 181 TYR 0.013 0.001 TYR B 125 ARG 0.009 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8660 (t80) cc_final: 0.8396 (t80) REVERT: A 65 MET cc_start: 0.4842 (ptm) cc_final: 0.4400 (ptm) REVERT: A 71 MET cc_start: 0.8227 (mtm) cc_final: 0.7936 (mtt) REVERT: A 159 LYS cc_start: 0.8684 (tmmt) cc_final: 0.8290 (tppt) REVERT: A 195 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8901 (pt) REVERT: A 249 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8182 (ttp-170) REVERT: A 513 ARG cc_start: 0.7816 (mpt180) cc_final: 0.7607 (mpt180) REVERT: A 633 ILE cc_start: 0.7582 (tp) cc_final: 0.7262 (mt) REVERT: A 755 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6893 (mtp85) REVERT: A 757 GLU cc_start: 0.7284 (pt0) cc_final: 0.6845 (pt0) REVERT: B 123 MET cc_start: 0.7818 (ttt) cc_final: 0.7543 (ttm) REVERT: C 168 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: D 1 MET cc_start: 0.6950 (tmt) cc_final: 0.6743 (tmt) REVERT: E 129 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8735 (t) REVERT: E 139 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8286 (mt0) REVERT: E 147 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: E 176 MET cc_start: 0.8617 (mmm) cc_final: 0.8055 (mmp) REVERT: F 220 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8098 (ttpp) REVERT: F 301 MET cc_start: 0.6482 (ttm) cc_final: 0.6103 (tpp) outliers start: 44 outliers final: 11 residues processed: 284 average time/residue: 1.4061 time to fit residues: 442.1193 Evaluate side-chains 250 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.0570 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS B 179 HIS C 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18051 Z= 0.259 Angle : 0.613 11.754 24636 Z= 0.311 Chirality : 0.045 0.215 2724 Planarity : 0.005 0.049 2992 Dihedral : 15.328 177.327 3125 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.08 % Allowed : 19.43 % Favored : 77.49 % 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: -1.20 (0.18), residues: 2006 helix: 0.15 (0.19), residues: 797 sheet: -0.96 (0.27), residues: 311 loop : -1.56 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 393 HIS 0.007 0.001 HIS D 205 PHE 0.022 0.002 PHE E 15 TYR 0.019 0.002 TYR A 265 ARG 0.009 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8168 (mtm) cc_final: 0.7832 (mtt) REVERT: A 87 MET cc_start: 0.7740 (tmm) cc_final: 0.7488 (ttt) REVERT: A 91 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 158 VAL cc_start: 0.8515 (t) cc_final: 0.8261 (t) REVERT: A 159 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8278 (tppt) REVERT: A 195 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9016 (pt) REVERT: A 513 ARG cc_start: 0.7832 (mpt180) cc_final: 0.7589 (mpt180) REVERT: A 629 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: A 633 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (mt) REVERT: A 755 ARG cc_start: 0.7570 (mtp85) cc_final: 0.6972 (mtp85) REVERT: A 757 GLU cc_start: 0.7198 (pt0) cc_final: 0.6768 (pt0) REVERT: B 123 MET cc_start: 0.7712 (ttt) cc_final: 0.7422 (ttm) REVERT: C 77 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8690 (ttpp) REVERT: C 168 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 267 LYS cc_start: 0.8280 (pttm) cc_final: 0.7661 (ptmm) REVERT: D 185 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8052 (ptp-170) REVERT: E 129 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8789 (t) REVERT: E 139 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8443 (mt0) REVERT: E 147 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7156 (tm-30) outliers start: 51 outliers final: 22 residues processed: 282 average time/residue: 1.4118 time to fit residues: 440.8997 Evaluate side-chains 260 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN C 37 ASN D 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18051 Z= 0.383 Angle : 0.677 13.196 24636 Z= 0.346 Chirality : 0.048 0.245 2724 Planarity : 0.005 0.082 2992 Dihedral : 15.407 176.714 3125 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.80 % Allowed : 19.07 % Favored : 77.13 % 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: -1.24 (0.18), residues: 2006 helix: 0.07 (0.19), residues: 798 sheet: -0.90 (0.28), residues: 310 loop : -1.56 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.009 0.001 HIS D 205 PHE 0.022 0.002 PHE E 15 TYR 0.019 0.002 TYR A 265 ARG 0.009 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 235 time to evaluate : 1.966 Fit side-chains REVERT: A 71 MET cc_start: 0.8176 (mtm) cc_final: 0.7837 (mtt) REVERT: A 91 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8970 (tt) REVERT: A 158 VAL cc_start: 0.8489 (t) cc_final: 0.8228 (t) REVERT: A 159 LYS cc_start: 0.8660 (tmmt) cc_final: 0.8235 (tppt) REVERT: A 162 TRP cc_start: 0.8473 (t-100) cc_final: 0.8036 (t-100) REVERT: A 195 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9089 (pt) REVERT: A 755 ARG cc_start: 0.7628 (mtp85) cc_final: 0.6897 (mtp85) REVERT: A 757 GLU cc_start: 0.7356 (pt0) cc_final: 0.6798 (pt0) REVERT: B 123 MET cc_start: 0.7723 (ttt) cc_final: 0.7388 (ttm) REVERT: C 168 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: C 236 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8546 (m) REVERT: C 267 LYS cc_start: 0.8332 (pttm) cc_final: 0.7704 (ptmm) REVERT: D 185 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8090 (ptp-170) REVERT: E 129 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8836 (t) REVERT: E 147 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: F 215 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7768 (mttp) REVERT: F 302 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6095 (mmtm) outliers start: 63 outliers final: 30 residues processed: 275 average time/residue: 1.4114 time to fit residues: 429.4634 Evaluate side-chains 255 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18051 Z= 0.176 Angle : 0.569 11.116 24636 Z= 0.291 Chirality : 0.043 0.195 2724 Planarity : 0.004 0.047 2992 Dihedral : 15.214 177.039 3125 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.02 % Allowed : 20.52 % Favored : 76.46 % 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: -0.86 (0.18), residues: 2006 helix: 0.50 (0.19), residues: 794 sheet: -0.85 (0.28), residues: 297 loop : -1.41 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 131 HIS 0.005 0.001 HIS F 33 PHE 0.013 0.001 PHE E 159 TYR 0.014 0.001 TYR A 552 ARG 0.010 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 241 time to evaluate : 1.887 Fit side-chains REVERT: A 71 MET cc_start: 0.8181 (mtm) cc_final: 0.7829 (mtt) REVERT: A 91 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8983 (tp) REVERT: A 158 VAL cc_start: 0.8433 (t) cc_final: 0.8154 (t) REVERT: A 195 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8968 (pt) REVERT: A 407 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: A 443 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 513 ARG cc_start: 0.7802 (mpt180) cc_final: 0.7594 (mpt180) REVERT: A 629 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6617 (mt-10) REVERT: A 755 ARG cc_start: 0.7509 (mtp85) cc_final: 0.6799 (mtp85) REVERT: A 757 GLU cc_start: 0.7205 (pt0) cc_final: 0.6666 (pt0) REVERT: C 77 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8659 (ttpp) REVERT: C 168 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: C 236 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8178 (m) REVERT: C 267 LYS cc_start: 0.8262 (pttm) cc_final: 0.7605 (ptmm) REVERT: D 107 ARG cc_start: 0.7770 (mpt-90) cc_final: 0.7518 (mtt180) REVERT: D 185 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8086 (ptp-170) REVERT: E 129 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8782 (t) REVERT: E 147 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: F 215 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7874 (mttp) REVERT: F 301 MET cc_start: 0.6536 (ttm) cc_final: 0.6125 (tpp) REVERT: F 391 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7681 (ptm) outliers start: 50 outliers final: 18 residues processed: 275 average time/residue: 1.4329 time to fit residues: 437.1220 Evaluate side-chains 257 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18051 Z= 0.165 Angle : 0.567 9.268 24636 Z= 0.289 Chirality : 0.043 0.206 2724 Planarity : 0.004 0.047 2992 Dihedral : 15.173 177.522 3125 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.17 % Allowed : 21.97 % Favored : 75.86 % 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: -0.64 (0.19), residues: 2006 helix: 0.79 (0.19), residues: 782 sheet: -0.87 (0.27), residues: 317 loop : -1.31 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 131 HIS 0.004 0.001 HIS F 254 PHE 0.013 0.001 PHE E 159 TYR 0.014 0.001 TYR A 552 ARG 0.015 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 1.829 Fit side-chains REVERT: A 71 MET cc_start: 0.8206 (mtm) cc_final: 0.7844 (mtt) REVERT: A 91 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8971 (tp) REVERT: A 158 VAL cc_start: 0.8421 (t) cc_final: 0.8114 (t) REVERT: A 195 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8962 (pt) REVERT: A 407 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: A 443 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8149 (tt) REVERT: A 629 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6027 (pt0) REVERT: A 755 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6780 (mtp85) REVERT: A 757 GLU cc_start: 0.7184 (pt0) cc_final: 0.6657 (pt0) REVERT: B 123 MET cc_start: 0.7656 (ttt) cc_final: 0.7424 (ttm) REVERT: C 168 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 236 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8182 (m) REVERT: C 267 LYS cc_start: 0.8264 (pttm) cc_final: 0.7609 (ptmm) REVERT: E 129 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8773 (t) REVERT: E 147 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: F 215 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7833 (mttp) REVERT: F 301 MET cc_start: 0.6555 (ttm) cc_final: 0.5885 (tpp) REVERT: F 302 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6233 (mmtt) REVERT: F 391 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7586 (ptm) outliers start: 36 outliers final: 16 residues processed: 260 average time/residue: 1.4077 time to fit residues: 405.1262 Evaluate side-chains 246 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18051 Z= 0.162 Angle : 0.558 9.106 24636 Z= 0.286 Chirality : 0.042 0.195 2724 Planarity : 0.004 0.048 2992 Dihedral : 15.085 177.327 3125 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 2.29 % Allowed : 21.79 % Favored : 75.92 % 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: -0.52 (0.19), residues: 2006 helix: 0.93 (0.19), residues: 781 sheet: -0.85 (0.27), residues: 317 loop : -1.26 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 131 HIS 0.004 0.001 HIS F 254 PHE 0.013 0.001 PHE E 159 TYR 0.012 0.001 TYR E 90 ARG 0.011 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.872 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 195 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8949 (pt) REVERT: A 407 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: A 443 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 755 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6769 (mtp85) REVERT: A 757 GLU cc_start: 0.7139 (pt0) cc_final: 0.6619 (pt0) REVERT: C 168 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 236 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8219 (m) REVERT: C 267 LYS cc_start: 0.8254 (pttm) cc_final: 0.7620 (ptmm) REVERT: E 129 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8783 (t) REVERT: E 147 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: F 31 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6185 (pt) REVERT: F 100 ILE cc_start: 0.6590 (mm) cc_final: 0.6351 (mm) REVERT: F 215 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7864 (mttp) REVERT: F 301 MET cc_start: 0.6536 (ttm) cc_final: 0.5900 (tpp) REVERT: F 391 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7619 (ptm) outliers start: 38 outliers final: 16 residues processed: 252 average time/residue: 1.3383 time to fit residues: 375.3429 Evaluate side-chains 247 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 456 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18051 Z= 0.171 Angle : 0.563 9.046 24636 Z= 0.287 Chirality : 0.043 0.197 2724 Planarity : 0.004 0.048 2992 Dihedral : 15.053 177.399 3123 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 1.99 % Allowed : 22.27 % Favored : 75.74 % 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: -0.44 (0.19), residues: 2006 helix: 1.01 (0.19), residues: 782 sheet: -0.82 (0.27), residues: 317 loop : -1.24 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 131 HIS 0.006 0.001 HIS F 254 PHE 0.013 0.001 PHE E 159 TYR 0.014 0.001 TYR E 90 ARG 0.014 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 2.052 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8983 (tp) REVERT: A 195 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8963 (pt) REVERT: A 407 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: A 443 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 755 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6756 (mtp85) REVERT: A 757 GLU cc_start: 0.7127 (pt0) cc_final: 0.6601 (pt0) REVERT: C 168 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 236 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8242 (m) REVERT: E 129 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8775 (t) REVERT: E 147 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: F 31 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.6151 (pt) REVERT: F 100 ILE cc_start: 0.6664 (mm) cc_final: 0.6453 (mm) REVERT: F 215 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7951 (mttp) REVERT: F 301 MET cc_start: 0.6518 (ttm) cc_final: 0.5859 (tpp) REVERT: F 302 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6024 (mmtt) REVERT: F 391 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7666 (ptm) outliers start: 33 outliers final: 17 residues processed: 250 average time/residue: 1.3741 time to fit residues: 383.2012 Evaluate side-chains 247 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131405 restraints weight = 19233.875| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.96 r_work: 0.3171 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18051 Z= 0.176 Angle : 0.571 11.831 24636 Z= 0.291 Chirality : 0.043 0.198 2724 Planarity : 0.004 0.058 2992 Dihedral : 15.015 177.458 3123 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 1.81 % Allowed : 22.93 % Favored : 75.26 % 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: -0.41 (0.19), residues: 2006 helix: 1.05 (0.19), residues: 781 sheet: -0.78 (0.28), residues: 307 loop : -1.22 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 393 HIS 0.006 0.001 HIS F 254 PHE 0.013 0.001 PHE E 159 TYR 0.015 0.001 TYR A 552 ARG 0.017 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7387.93 seconds wall clock time: 129 minutes 31.54 seconds (7771.54 seconds total)