Starting phenix.real_space_refine on Sat Mar 16 18:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d37_27155/03_2024/8d37_27155_neut_updated.pdb" } resolution = 2.65 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= 0.339 sd= 0.592 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 Ca 1 9.91 5 P 51 5.49 5 S 82 5.16 5 C 9605 2.51 5 N 2690 2.21 5 O 2885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.43, per 1000 atoms: 0.55 Number of scatterers: 15314 At special positions: 0 Unit cell: (113.05, 112.2, 153, 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) Ca 1 19.99 S 82 16.00 P 51 15.00 O 2885 8.00 N 2690 7.00 C 9605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.41 Conformation dependent library (CDL) restraints added in 2.6 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 10 sheets defined 42.8% alpha, 13.7% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 6.75 Creating SS restraints... Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 135 through 158 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.787A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.564A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 417 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.534A pdb=" N ALA A 425 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 481 removed outlier: 3.703A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.636A pdb=" N ASP A 542 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET A 544 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 547 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 551 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 553 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.722A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.797A pdb=" N LEU A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Proline residue: A 772 - end of helix Processing helix chain 'A' and resid 787 through 809 removed outlier: 4.950A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.516A pdb=" N LEU A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.514A pdb=" N PHE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 989 Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1085 through 1088 No H-bonds generated for 'chain 'A' and resid 1085 through 1088' Processing helix chain 'A' and resid 1093 through 1122 removed outlier: 3.617A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1168 removed outlier: 4.520A pdb=" N TYR A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1205 through 1208 No H-bonds generated for 'chain 'A' and resid 1205 through 1208' Processing helix chain 'A' and resid 1220 through 1227 Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.355A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 4.573A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.926A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 392 through 409 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 468 through 484 removed outlier: 4.447A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.635A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 177 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 removed outlier: 4.352A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 266 removed outlier: 4.495A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 392 through 409 removed outlier: 3.559A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.633A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.256A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.936A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER A 216 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ALA A 194 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 265 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 197 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 267 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL A 199 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 290 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY A 268 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 292 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 435 through 438 Processing sheet with id= C, first strand: chain 'A' and resid 612 through 615 removed outlier: 6.842A pdb=" N GLY A 746 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 5.591A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.737A pdb=" N GLY B 207 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER B 337 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN B 305 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 339 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 303 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP B 341 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B 301 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 326 Processing sheet with id= G, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.939A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 439 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.928A pdb=" N GLY C 207 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 307 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER C 337 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN C 305 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN C 339 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU C 303 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP C 341 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU C 301 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU C 289 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR C 302 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN C 287 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TRP C 304 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS C 285 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 323 through 326 Processing sheet with id= J, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.273A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 439 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASP C 386 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 441 " --> pdb=" O ASP C 386 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4753 1.34 - 1.46: 2701 1.46 - 1.58: 8119 1.58 - 1.70: 95 1.70 - 1.82: 130 Bond restraints: 15798 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.579 1.799 -0.220 1.50e-02 4.44e+03 2.16e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.706 -0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.329 0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C4' DCP A1302 " pdb=" C5' DCP A1302 " ideal model delta sigma weight residual 1.508 1.560 -0.052 1.10e-02 8.26e+03 2.25e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.08e+01 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 91.12 - 99.84: 5 99.84 - 108.55: 1392 108.55 - 117.27: 10293 117.27 - 125.99: 9414 125.99 - 134.71: 516 Bond angle restraints: 21620 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 133.36 6.51 1.00e+00 1.00e+00 4.24e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.88 6.60 1.14e+00 7.76e-01 3.38e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 116.91 -9.97 1.88e+00 2.83e-01 2.81e+01 angle pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 101.57 93.68 7.89 1.54e+00 4.24e-01 2.64e+01 angle pdb=" O3A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 102.67 91.12 11.55 2.38e+00 1.77e-01 2.36e+01 ... (remaining 21615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 8632 17.05 - 34.10: 477 34.10 - 51.15: 128 51.15 - 68.20: 69 68.20 - 85.25: 6 Dihedral angle restraints: 9312 sinusoidal: 4165 harmonic: 5147 Sorted by residual: dihedral pdb=" CA ASP B 159 " pdb=" C ASP B 159 " pdb=" N LYS B 160 " pdb=" CA LYS B 160 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS C 164 " pdb=" C LYS C 164 " pdb=" N GLU C 165 " pdb=" CA GLU C 165 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 125.77 -32.77 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1619 0.031 - 0.062: 479 0.062 - 0.094: 133 0.094 - 0.125: 90 0.125 - 0.156: 9 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' DCP A1302 " pdb=" C3' DCP A1302 " pdb=" C5' DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL B 443 " pdb=" N VAL B 443 " pdb=" C VAL B 443 " pdb=" CB VAL B 443 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2327 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 435 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO A 436 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A1200 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 8 " 0.017 2.00e-02 2.50e+03 6.96e-03 1.45e+00 pdb=" N9 DG P 8 " -0.015 2.00e-02 2.50e+03 pdb=" C8 DG P 8 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG P 8 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG P 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG P 8 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG P 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 8 " -0.002 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 121 2.55 - 3.14: 12211 3.14 - 3.72: 23830 3.72 - 4.31: 33483 4.31 - 4.90: 54695 Nonbonded interactions: 124340 Sorted by model distance: nonbonded pdb=" OD1 ASP A 904 " pdb=" OG1 THR A 914 " model vdw 1.962 2.440 nonbonded pdb=" OE1 GLU A 895 " pdb=" OH TYR A 955 " model vdw 2.040 2.440 nonbonded pdb=" NZ LYS A 461 " pdb=" O LYS B 265 " model vdw 2.130 2.520 nonbonded pdb=" O MET C 435 " pdb=" OG SER C 436 " model vdw 2.137 2.440 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.165 2.440 ... (remaining 124335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 7.790 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 46.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.003 0.220 15798 Z= 0.178 Angle : 0.519 12.913 21620 Z= 0.289 Chirality : 0.037 0.156 2330 Planarity : 0.003 0.037 2604 Dihedral : 12.722 85.251 5987 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.32 % Allowed : 2.07 % Favored : 97.61 % 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: 0.95 (0.21), residues: 1758 helix: 1.14 (0.21), residues: 713 sheet: 0.81 (0.32), residues: 240 loop : 0.24 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS A 138 PHE 0.011 0.001 PHE A 197 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 524 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7104 (mt) cc_final: 0.6750 (mt) REVERT: A 138 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6344 (t-90) REVERT: A 296 SER cc_start: 0.8246 (p) cc_final: 0.7896 (m) REVERT: A 382 MET cc_start: 0.8198 (tpp) cc_final: 0.7757 (tpt) REVERT: A 466 LEU cc_start: 0.7422 (mp) cc_final: 0.7187 (tp) REVERT: A 602 LEU cc_start: 0.8072 (mt) cc_final: 0.7863 (mt) REVERT: A 818 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7638 (ttm-80) REVERT: B 74 GLN cc_start: 0.7384 (tt0) cc_final: 0.6979 (tp40) REVERT: B 152 THR cc_start: 0.8107 (p) cc_final: 0.7691 (t) REVERT: B 241 TRP cc_start: 0.5727 (t-100) cc_final: 0.5098 (t-100) REVERT: B 259 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7305 (mmp-170) REVERT: B 411 ILE cc_start: 0.8489 (mt) cc_final: 0.8252 (mm) REVERT: B 435 MET cc_start: 0.7375 (mtp) cc_final: 0.7141 (mtm) REVERT: B 465 MET cc_start: 0.8500 (mmm) cc_final: 0.7685 (mmm) outliers start: 5 outliers final: 3 residues processed: 528 average time/residue: 1.1796 time to fit residues: 687.9674 Evaluate side-chains 404 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 399 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A1059 ASN A1098 ASN A1110 HIS B 124 GLN B 132 HIS B 216 HIS B 397 GLN C 85 GLN C 258 HIS C 261 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15798 Z= 0.418 Angle : 0.775 9.750 21620 Z= 0.401 Chirality : 0.049 0.270 2330 Planarity : 0.007 0.059 2604 Dihedral : 15.092 89.920 2488 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.46 % Allowed : 12.92 % Favored : 80.62 % 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: 0.21 (0.20), residues: 1758 helix: 0.66 (0.19), residues: 714 sheet: 0.39 (0.30), residues: 245 loop : -0.31 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 918 HIS 0.009 0.002 HIS C 187 PHE 0.020 0.003 PHE B 219 TYR 0.020 0.003 TYR B 291 ARG 0.020 0.001 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 388 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7244 (mt) cc_final: 0.6915 (mt) REVERT: A 138 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6361 (t-90) REVERT: A 299 MET cc_start: 0.8304 (tpt) cc_final: 0.8067 (tpt) REVERT: A 460 LYS cc_start: 0.8241 (mttm) cc_final: 0.8032 (mttm) REVERT: A 490 TRP cc_start: 0.7670 (m100) cc_final: 0.7413 (m100) REVERT: A 769 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: A 866 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7656 (mtp-110) REVERT: A 966 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 993 ARG cc_start: 0.5278 (tpm-80) cc_final: 0.4929 (tpt170) REVERT: A 1061 LEU cc_start: 0.8116 (mt) cc_final: 0.7896 (mt) REVERT: B 74 GLN cc_start: 0.7683 (tt0) cc_final: 0.7444 (tt0) REVERT: B 122 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7497 (mtt-85) REVERT: C 185 LEU cc_start: 0.8261 (mm) cc_final: 0.8047 (mt) REVERT: C 195 ASN cc_start: 0.7783 (t0) cc_final: 0.7464 (t0) REVERT: C 197 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8097 (tt) REVERT: C 252 LEU cc_start: 0.8296 (tt) cc_final: 0.8002 (tp) REVERT: C 256 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 483 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8385 (ttmt) outliers start: 100 outliers final: 46 residues processed: 445 average time/residue: 1.1313 time to fit residues: 557.4424 Evaluate side-chains 425 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 371 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 483 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 569 HIS A 803 ASN A 968 GLN A1059 ASN A1110 HIS B 124 GLN B 397 GLN C 85 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15798 Z= 0.392 Angle : 0.736 9.118 21620 Z= 0.387 Chirality : 0.047 0.187 2330 Planarity : 0.007 0.055 2604 Dihedral : 15.290 88.762 2481 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.91 % Allowed : 16.54 % Favored : 76.55 % 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: -0.17 (0.20), residues: 1758 helix: 0.39 (0.19), residues: 717 sheet: 0.41 (0.31), residues: 239 loop : -0.65 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 918 HIS 0.008 0.002 HIS B 454 PHE 0.018 0.003 PHE C 293 TYR 0.016 0.003 TYR B 291 ARG 0.006 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 384 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7286 (mt) cc_final: 0.6935 (mt) REVERT: A 138 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6359 (t-90) REVERT: A 178 TYR cc_start: 0.6145 (m-80) cc_final: 0.5910 (m-80) REVERT: A 430 MET cc_start: 0.7306 (ttp) cc_final: 0.7048 (ttp) REVERT: A 490 TRP cc_start: 0.7610 (m100) cc_final: 0.7314 (m100) REVERT: A 769 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: A 866 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7810 (mtp-110) REVERT: A 927 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7542 (mtm-85) REVERT: A 1061 LEU cc_start: 0.8130 (mt) cc_final: 0.7923 (mt) REVERT: A 1163 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7208 (tpt) REVERT: B 74 GLN cc_start: 0.7823 (tt0) cc_final: 0.7595 (tt0) REVERT: B 122 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7417 (mtt-85) REVERT: C 252 LEU cc_start: 0.8325 (tt) cc_final: 0.8037 (tp) REVERT: C 433 ASP cc_start: 0.8027 (m-30) cc_final: 0.7793 (m-30) outliers start: 107 outliers final: 57 residues processed: 434 average time/residue: 1.2109 time to fit residues: 580.7020 Evaluate side-chains 430 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 367 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 803 ASN A 922 GLN A1059 ASN A1110 HIS B 124 GLN B 184 ASN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15798 Z= 0.272 Angle : 0.653 9.783 21620 Z= 0.342 Chirality : 0.043 0.154 2330 Planarity : 0.006 0.047 2604 Dihedral : 15.160 89.331 2481 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 7.17 % Allowed : 17.76 % Favored : 75.06 % 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: -0.02 (0.20), residues: 1758 helix: 0.60 (0.19), residues: 715 sheet: 0.39 (0.31), residues: 240 loop : -0.63 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 241 HIS 0.005 0.001 HIS A 565 PHE 0.017 0.002 PHE B 403 TYR 0.013 0.002 TYR B 291 ARG 0.008 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 379 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6315 (t-90) REVERT: A 178 TYR cc_start: 0.6111 (m-80) cc_final: 0.5910 (m-80) REVERT: A 430 MET cc_start: 0.7241 (ttp) cc_final: 0.7000 (ttp) REVERT: A 490 TRP cc_start: 0.7597 (m100) cc_final: 0.7323 (m100) REVERT: A 552 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7276 (mt) REVERT: A 769 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: A 866 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7792 (mtp-110) REVERT: A 927 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7555 (mtm-85) REVERT: A 966 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 1061 LEU cc_start: 0.8121 (mt) cc_final: 0.7889 (mt) REVERT: A 1163 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7192 (tpt) REVERT: B 74 GLN cc_start: 0.7768 (tt0) cc_final: 0.7545 (tt0) REVERT: B 342 LEU cc_start: 0.7844 (mm) cc_final: 0.7590 (mt) REVERT: C 252 LEU cc_start: 0.8303 (tt) cc_final: 0.8044 (tp) REVERT: C 256 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 259 ARG cc_start: 0.7865 (mmm160) cc_final: 0.7595 (mmm160) REVERT: C 433 ASP cc_start: 0.8020 (m-30) cc_final: 0.7791 (m-30) outliers start: 111 outliers final: 59 residues processed: 434 average time/residue: 1.1604 time to fit residues: 559.0008 Evaluate side-chains 432 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 365 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 922 GLN A 968 GLN A1110 HIS B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15798 Z= 0.316 Angle : 0.688 11.823 21620 Z= 0.359 Chirality : 0.044 0.178 2330 Planarity : 0.006 0.048 2604 Dihedral : 15.229 89.868 2481 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 7.36 % Allowed : 18.86 % Favored : 73.77 % 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: -0.18 (0.20), residues: 1758 helix: 0.50 (0.19), residues: 714 sheet: 0.30 (0.31), residues: 240 loop : -0.74 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 241 HIS 0.006 0.001 HIS B 454 PHE 0.016 0.002 PHE C 273 TYR 0.020 0.002 TYR C 315 ARG 0.008 0.001 ARG A1234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 378 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7189 (mt) cc_final: 0.6821 (mt) REVERT: A 138 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6333 (t-90) REVERT: A 430 MET cc_start: 0.7259 (ttp) cc_final: 0.7003 (ttp) REVERT: A 490 TRP cc_start: 0.7540 (m100) cc_final: 0.7296 (m100) REVERT: A 552 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7369 (mt) REVERT: A 769 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: A 866 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7799 (mtp-110) REVERT: A 927 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7550 (mtm-85) REVERT: A 1163 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7206 (tpt) REVERT: B 74 GLN cc_start: 0.7808 (tt0) cc_final: 0.7586 (tt0) REVERT: B 236 GLU cc_start: 0.6953 (pm20) cc_final: 0.6298 (mp0) REVERT: B 342 LEU cc_start: 0.7858 (mm) cc_final: 0.7617 (mt) REVERT: C 252 LEU cc_start: 0.8304 (tt) cc_final: 0.8075 (tp) REVERT: C 256 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 259 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7627 (mmm160) outliers start: 114 outliers final: 70 residues processed: 440 average time/residue: 1.1630 time to fit residues: 566.7638 Evaluate side-chains 448 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 371 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1233 LYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 0.0170 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.0370 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 287 ASN B 397 GLN C 85 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15798 Z= 0.195 Angle : 0.621 12.581 21620 Z= 0.320 Chirality : 0.041 0.164 2330 Planarity : 0.005 0.048 2604 Dihedral : 15.002 84.155 2481 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.49 % Allowed : 21.12 % Favored : 73.39 % 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: 0.19 (0.20), residues: 1758 helix: 0.84 (0.19), residues: 711 sheet: 0.50 (0.32), residues: 232 loop : -0.56 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 241 HIS 0.006 0.001 HIS A 71 PHE 0.014 0.001 PHE B 403 TYR 0.014 0.002 TYR C 429 ARG 0.008 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 387 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7091 (m-70) REVERT: A 138 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.6298 (t-90) REVERT: A 296 SER cc_start: 0.8317 (p) cc_final: 0.7844 (m) REVERT: A 490 TRP cc_start: 0.7491 (m100) cc_final: 0.7245 (m100) REVERT: A 769 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: A 866 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7776 (mtp-110) REVERT: B 74 GLN cc_start: 0.7725 (tt0) cc_final: 0.7501 (tt0) REVERT: B 236 GLU cc_start: 0.6866 (pm20) cc_final: 0.6540 (mt-10) REVERT: B 366 ASN cc_start: 0.5834 (m-40) cc_final: 0.5538 (m-40) REVERT: C 252 LEU cc_start: 0.8311 (tt) cc_final: 0.8086 (tp) REVERT: C 256 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 442 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6456 (tp) outliers start: 85 outliers final: 42 residues processed: 433 average time/residue: 1.1968 time to fit residues: 573.5749 Evaluate side-chains 413 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 365 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 397 GLN C 258 HIS C 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15798 Z= 0.300 Angle : 0.693 13.845 21620 Z= 0.356 Chirality : 0.044 0.168 2330 Planarity : 0.006 0.075 2604 Dihedral : 15.115 84.504 2481 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.68 % Allowed : 22.61 % Favored : 71.71 % 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: -0.02 (0.20), residues: 1758 helix: 0.64 (0.19), residues: 716 sheet: 0.48 (0.32), residues: 233 loop : -0.69 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 241 HIS 0.013 0.001 HIS A 71 PHE 0.021 0.002 PHE C 273 TYR 0.022 0.002 TYR C 315 ARG 0.017 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 368 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6333 (t-90) REVERT: A 178 TYR cc_start: 0.6274 (m-80) cc_final: 0.6030 (m-80) REVERT: A 296 SER cc_start: 0.8333 (p) cc_final: 0.7874 (m) REVERT: A 444 TYR cc_start: 0.7805 (t80) cc_final: 0.7462 (t80) REVERT: A 490 TRP cc_start: 0.7520 (m100) cc_final: 0.7308 (m100) REVERT: A 769 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: A 866 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7766 (mtp-110) REVERT: A 927 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7551 (mtm-85) REVERT: A 1163 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: B 74 GLN cc_start: 0.7775 (tt0) cc_final: 0.7571 (tt0) REVERT: B 236 GLU cc_start: 0.6934 (pm20) cc_final: 0.6287 (mp0) REVERT: C 252 LEU cc_start: 0.8322 (tt) cc_final: 0.8111 (tp) REVERT: C 256 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8001 (tp) outliers start: 88 outliers final: 59 residues processed: 414 average time/residue: 1.1748 time to fit residues: 539.5189 Evaluate side-chains 419 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 354 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 258 HIS B 287 ASN B 397 GLN C 258 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15798 Z= 0.209 Angle : 0.654 16.521 21620 Z= 0.331 Chirality : 0.041 0.157 2330 Planarity : 0.005 0.047 2604 Dihedral : 14.987 80.134 2481 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.78 % Allowed : 23.71 % Favored : 71.51 % 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: 0.20 (0.20), residues: 1758 helix: 0.83 (0.20), residues: 709 sheet: 0.66 (0.33), residues: 225 loop : -0.58 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 241 HIS 0.005 0.001 HIS A 71 PHE 0.023 0.002 PHE B 126 TYR 0.017 0.002 TYR C 429 ARG 0.008 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 366 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6304 (t-90) REVERT: A 296 SER cc_start: 0.8295 (p) cc_final: 0.7826 (m) REVERT: A 444 TYR cc_start: 0.7780 (t80) cc_final: 0.7499 (t80) REVERT: A 490 TRP cc_start: 0.7467 (m100) cc_final: 0.7224 (m100) REVERT: A 769 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: A 866 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7723 (mtp-110) REVERT: A 868 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7419 (p0) REVERT: A 927 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: B 74 GLN cc_start: 0.7738 (tt0) cc_final: 0.7518 (tt0) REVERT: B 236 GLU cc_start: 0.6855 (pm20) cc_final: 0.6233 (mp0) REVERT: B 472 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7772 (ttpp) REVERT: C 252 LEU cc_start: 0.8301 (tt) cc_final: 0.8081 (tp) REVERT: C 256 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7982 (tp) outliers start: 74 outliers final: 52 residues processed: 411 average time/residue: 1.1923 time to fit residues: 541.7848 Evaluate side-chains 418 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 359 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 106 optimal weight: 0.0030 chunk 171 optimal weight: 6.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN B 184 ASN B 397 GLN C 258 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15798 Z= 0.264 Angle : 0.698 17.621 21620 Z= 0.353 Chirality : 0.043 0.181 2330 Planarity : 0.006 0.088 2604 Dihedral : 15.044 79.582 2481 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.17 % Allowed : 23.84 % Favored : 70.99 % 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: 0.07 (0.20), residues: 1758 helix: 0.73 (0.19), residues: 709 sheet: 0.42 (0.32), residues: 240 loop : -0.61 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 241 HIS 0.009 0.001 HIS A 71 PHE 0.015 0.002 PHE C 273 TYR 0.024 0.002 TYR C 315 ARG 0.018 0.001 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 360 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6356 (t-90) REVERT: A 296 SER cc_start: 0.8253 (p) cc_final: 0.7738 (m) REVERT: A 444 TYR cc_start: 0.7779 (t80) cc_final: 0.7483 (t80) REVERT: A 490 TRP cc_start: 0.7488 (m100) cc_final: 0.7272 (m100) REVERT: A 769 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: A 866 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7729 (mtp-110) REVERT: A 868 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7420 (p0) REVERT: A 916 PHE cc_start: 0.7275 (t80) cc_final: 0.7024 (t80) REVERT: A 927 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: A 1185 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8060 (mm) REVERT: B 74 GLN cc_start: 0.7760 (tt0) cc_final: 0.7545 (tt0) REVERT: B 236 GLU cc_start: 0.6911 (pm20) cc_final: 0.6273 (mt-10) REVERT: B 408 GLU cc_start: 0.7020 (tp30) cc_final: 0.6808 (tp30) REVERT: B 472 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7787 (ttpp) REVERT: C 252 LEU cc_start: 0.8313 (tt) cc_final: 0.8049 (tp) REVERT: C 256 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7976 (tp) REVERT: C 437 ILE cc_start: 0.6934 (mt) cc_final: 0.6694 (mt) outliers start: 80 outliers final: 55 residues processed: 407 average time/residue: 1.1583 time to fit residues: 521.8747 Evaluate side-chains 419 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 356 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 6.9990 chunk 81 optimal weight: 0.0060 chunk 119 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 258 HIS C 258 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15798 Z= 0.261 Angle : 0.860 59.198 21620 Z= 0.470 Chirality : 0.043 0.184 2330 Planarity : 0.006 0.088 2604 Dihedral : 15.041 79.297 2481 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.84 % Allowed : 24.68 % Favored : 70.48 % Cbeta Deviations : 0.06 % 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: 0.08 (0.20), residues: 1758 helix: 0.73 (0.19), residues: 709 sheet: 0.40 (0.32), residues: 243 loop : -0.60 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 241 HIS 0.010 0.001 HIS A 71 PHE 0.017 0.002 PHE C 273 TYR 0.019 0.002 TYR C 429 ARG 0.018 0.001 ARG A 650 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 357 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.6350 (t-90) REVERT: A 296 SER cc_start: 0.8249 (p) cc_final: 0.7733 (m) REVERT: A 444 TYR cc_start: 0.7775 (t80) cc_final: 0.7476 (t80) REVERT: A 490 TRP cc_start: 0.7481 (m100) cc_final: 0.7267 (m100) REVERT: A 769 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: A 866 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7725 (mtp-110) REVERT: A 868 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7439 (p0) REVERT: A 916 PHE cc_start: 0.7256 (t80) cc_final: 0.7012 (t80) REVERT: A 927 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7558 (mtm-85) REVERT: A 1185 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (mm) REVERT: B 74 GLN cc_start: 0.7755 (tt0) cc_final: 0.7536 (tt0) REVERT: B 236 GLU cc_start: 0.6898 (pm20) cc_final: 0.6278 (mt-10) REVERT: B 408 GLU cc_start: 0.7006 (tp30) cc_final: 0.6790 (tp30) REVERT: B 472 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7779 (ttpp) REVERT: C 252 LEU cc_start: 0.8309 (tt) cc_final: 0.8045 (tp) REVERT: C 256 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7966 (tp) REVERT: C 437 ILE cc_start: 0.6918 (mt) cc_final: 0.6679 (mt) outliers start: 75 outliers final: 56 residues processed: 403 average time/residue: 1.1571 time to fit residues: 518.5114 Evaluate side-chains 417 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 353 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.0060 chunk 126 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 264 GLN A 922 GLN A 968 GLN A1110 HIS A1157 ASN B 124 GLN C 258 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.133852 restraints weight = 29296.783| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.76 r_work: 0.3830 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15798 Z= 0.261 Angle : 0.860 59.198 21620 Z= 0.470 Chirality : 0.043 0.184 2330 Planarity : 0.006 0.088 2604 Dihedral : 15.041 79.297 2481 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.39 % Allowed : 25.19 % Favored : 70.41 % Cbeta Deviations : 0.06 % 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: 0.08 (0.20), residues: 1758 helix: 0.73 (0.19), residues: 709 sheet: 0.40 (0.32), residues: 243 loop : -0.60 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 241 HIS 0.010 0.001 HIS A 71 PHE 0.017 0.002 PHE C 273 TYR 0.019 0.002 TYR C 429 ARG 0.018 0.001 ARG A 650 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7928.09 seconds wall clock time: 139 minutes 24.50 seconds (8364.50 seconds total)