Starting phenix.real_space_refine on Fri May 23 16:11:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785.map" model { file = "/net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ark_43785/05_2025/9ark_43785_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 15481 2.51 5 N 3961 2.21 5 O 4671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24165 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9959 Classifications: {'peptide': 1245} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 34, 'TRANS': 1210} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 9662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9662 Classifications: {'peptide': 1163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1129} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4544 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 555} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 15.76, per 1000 atoms: 0.65 Number of scatterers: 24165 At special positions: 0 Unit cell: (138.688, 167.844, 180.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 4671 8.00 N 3961 7.00 C 15481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 3.0 seconds 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 34 sheets defined 35.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.907A pdb=" N PHE A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 97 removed outlier: 3.723A pdb=" N ASN A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.623A pdb=" N LEU A 260 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.522A pdb=" N VAL A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.521A pdb=" N ASP A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 3.697A pdb=" N THR A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 removed outlier: 3.636A pdb=" N VAL A 382 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN A 383 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.912A pdb=" N SER A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 443 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 443' Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.891A pdb=" N ILE A 448 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.876A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.612A pdb=" N ASN A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.613A pdb=" N SER A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 614 through 620 removed outlier: 3.706A pdb=" N ASN A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.506A pdb=" N ALA A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 659 through 693 Processing helix chain 'A' and resid 693 through 726 removed outlier: 3.897A pdb=" N TYR A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 781 removed outlier: 4.054A pdb=" N ASN A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 760 " --> pdb=" O ASN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 800 removed outlier: 3.506A pdb=" N GLU A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 4.180A pdb=" N LEU A 804 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 836 through 849 removed outlier: 5.628A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1223 through 1228 removed outlier: 3.780A pdb=" N HIS A1228 " --> pdb=" O TRP A1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 71 through 92 removed outlier: 4.055A pdb=" N ASN B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.550A pdb=" N GLU B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.756A pdb=" N TYR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 252 through 273 removed outlier: 3.854A pdb=" N ILE B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.662A pdb=" N ILE B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.921A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.828A pdb=" N LYS B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.697A pdb=" N LYS B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.551A pdb=" N ILE B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 465 through 473 removed outlier: 3.539A pdb=" N GLN B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.568A pdb=" N VAL B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 511 Processing helix chain 'B' and resid 519 through 539 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 579 through 583 removed outlier: 3.693A pdb=" N ILE B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 641 removed outlier: 3.566A pdb=" N LEU B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 677 Processing helix chain 'B' and resid 681 through 725 removed outlier: 3.628A pdb=" N LEU B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 752 removed outlier: 3.802A pdb=" N GLN B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 750 " --> pdb=" O LYS B 746 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 766 removed outlier: 3.594A pdb=" N MET B 765 " --> pdb=" O SER B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 778 through 787 removed outlier: 4.167A pdb=" N PHE B 786 " --> pdb=" O MET B 782 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 removed outlier: 3.784A pdb=" N LEU B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 861 removed outlier: 3.612A pdb=" N GLU B 860 " --> pdb=" O ASP B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1003 Processing helix chain 'B' and resid 1152 through 1156 Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 349 through 355 removed outlier: 4.560A pdb=" N TRP C 354 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.922A pdb=" N LEU C 412 " --> pdb=" O ARG C 408 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.516A pdb=" N HIS C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR C 433 " --> pdb=" O HIS C 429 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 545 through 551 removed outlier: 3.543A pdb=" N THR C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 568 Processing helix chain 'C' and resid 576 through 587 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.526A pdb=" N GLU C 608 " --> pdb=" O ASN C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 634 removed outlier: 3.590A pdb=" N SER C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 652 removed outlier: 3.778A pdb=" N LEU C 646 " --> pdb=" O SER C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 674 removed outlier: 3.754A pdb=" N VAL C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 3.543A pdb=" N LEU C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 702 Processing helix chain 'C' and resid 705 through 714 Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 144 removed outlier: 3.648A pdb=" N GLU A 133 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASN A 34 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 41 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 36 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP A 40 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 149 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.954A pdb=" N LYS A 356 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 430 removed outlier: 7.209A pdb=" N ILE A 408 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS A 512 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG A 410 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 536 through 538 removed outlier: 6.149A pdb=" N ASN A 536 " --> pdb=" O ILE A 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AB1, first strand: chain 'A' and resid 851 through 857 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 862 through 864 current: chain 'A' and resid 887 through 891 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 887 through 891 current: chain 'A' and resid 990 through 997 removed outlier: 3.504A pdb=" N LYS A1004 " --> pdb=" O THR A 996 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A1007 " --> pdb=" O LEU A1011 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 871 through 876 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 896 through 901 current: chain 'A' and resid 949 through 955 Processing sheet with id=AB3, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 4.949A pdb=" N LYS A1126 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 15.198A pdb=" N VAL A1148 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N ALA A1164 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE A1150 " --> pdb=" O LEU A1162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1175 through 1177 current: chain 'A' and resid 1198 through 1203 removed outlier: 5.225A pdb=" N MET A1199 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN A1203 " --> pdb=" O ASN A1208 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A1208 " --> pdb=" O ASN A1203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1099 through 1100 Processing sheet with id=AB5, first strand: chain 'A' and resid 1114 through 1115 Processing sheet with id=AB6, first strand: chain 'B' and resid 18 through 22 removed outlier: 7.167A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 216 removed outlier: 6.112A pdb=" N LEU B 227 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU B 223 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 391 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC3, first strand: chain 'B' and resid 379 through 385 removed outlier: 6.602A pdb=" N LEU B 372 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 382 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 370 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASN B 384 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 368 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AC5, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AC6, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AC7, first strand: chain 'B' and resid 801 through 809 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 814 through 818 current: chain 'B' and resid 841 through 845 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 841 through 845 current: chain 'B' and resid 928 through 936 removed outlier: 6.192A pdb=" N LEU B 942 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 953 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 944 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 825 through 827 Processing sheet with id=AC9, first strand: chain 'B' and resid 883 through 890 removed outlier: 6.741A pdb=" N ILE B 897 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 887 " --> pdb=" O TRP B 895 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP B 895 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 889 " --> pdb=" O CYS B 893 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS B 893 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 905 " --> pdb=" O TYR B 898 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1020 through 1025 removed outlier: 4.635A pdb=" N LYS B1058 " --> pdb=" O LEU B1082 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B1082 " --> pdb=" O LYS B1058 " (cutoff:3.500A) removed outlier: 15.737A pdb=" N VAL B1077 " --> pdb=" O ILE B1091 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ILE B1091 " --> pdb=" O VAL B1077 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE B1079 " --> pdb=" O LEU B1089 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1098 through 1101 current: chain 'B' and resid 1122 through 1126 removed outlier: 14.142A pdb=" N LEU B1122 " --> pdb=" O LEU B1133 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N LEU B1133 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B1124 " --> pdb=" O ILE B1131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1033 through 1038 removed outlier: 3.569A pdb=" N SER B1045 " --> pdb=" O ASN B1034 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 357 through 364 removed outlier: 3.574A pdb=" N ALA C 420 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 197 through 204 removed outlier: 3.533A pdb=" N GLY C 213 " --> pdb=" O PHE C 198 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 215 current: chain 'C' and resid 228 through 242 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 245 through 248 current: chain 'C' and resid 280 through 286 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 280 through 286 current: chain 'C' and resid 716 through 717 Processing sheet with id=AD5, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AD6, first strand: chain 'C' and resid 446 through 448 removed outlier: 3.550A pdb=" N LYS C 483 " --> pdb=" O GLU C 494 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 490 through 494 current: chain 'C' and resid 508 through 523 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 526 through 533 current: chain 'C' and resid 593 through 599 Processing sheet with id=AD7, first strand: chain 'C' and resid 461 through 466 removed outlier: 4.096A pdb=" N PHE C 463 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA C 475 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS C 465 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 473 " --> pdb=" O LYS C 465 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2556 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.96 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6747 1.33 - 1.45: 4108 1.45 - 1.57: 13725 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 24665 Sorted by residual: bond pdb=" C ASP B 520 " pdb=" O ASP B 520 " ideal model delta sigma weight residual 1.235 1.214 0.021 1.26e-02 6.30e+03 2.85e+00 bond pdb=" C ALA A 480 " pdb=" N PRO A 481 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.28e+00 bond pdb=" C ILE B 517 " pdb=" O ILE B 517 " ideal model delta sigma weight residual 1.236 1.221 0.015 1.19e-02 7.06e+03 1.58e+00 bond pdb=" CB PRO A 481 " pdb=" CG PRO A 481 " ideal model delta sigma weight residual 1.492 1.554 -0.062 5.00e-02 4.00e+02 1.52e+00 bond pdb=" CB ASP B 520 " pdb=" CG ASP B 520 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.41e+00 ... (remaining 24660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 33085 1.53 - 3.06: 324 3.06 - 4.60: 46 4.60 - 6.13: 9 6.13 - 7.66: 3 Bond angle restraints: 33467 Sorted by residual: angle pdb=" N THR B 519 " pdb=" CA THR B 519 " pdb=" C THR B 519 " ideal model delta sigma weight residual 109.24 116.90 -7.66 1.67e+00 3.59e-01 2.10e+01 angle pdb=" N ILE B 517 " pdb=" CA ILE B 517 " pdb=" C ILE B 517 " ideal model delta sigma weight residual 109.34 116.29 -6.95 2.08e+00 2.31e-01 1.12e+01 angle pdb=" N PRO A 481 " pdb=" CA PRO A 481 " pdb=" C PRO A 481 " ideal model delta sigma weight residual 112.47 118.47 -6.00 2.06e+00 2.36e-01 8.50e+00 angle pdb=" CA TYR B 415 " pdb=" CB TYR B 415 " pdb=" CG TYR B 415 " ideal model delta sigma weight residual 113.90 118.86 -4.96 1.80e+00 3.09e-01 7.60e+00 angle pdb=" C HIS A1232 " pdb=" N THR A1233 " pdb=" CA THR A1233 " ideal model delta sigma weight residual 121.54 125.80 -4.26 1.91e+00 2.74e-01 4.98e+00 ... (remaining 33462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13860 17.66 - 35.33: 756 35.33 - 52.99: 159 52.99 - 70.65: 26 70.65 - 88.31: 9 Dihedral angle restraints: 14810 sinusoidal: 5935 harmonic: 8875 Sorted by residual: dihedral pdb=" CA ARG A1040 " pdb=" C ARG A1040 " pdb=" N TYR A1041 " pdb=" CA TYR A1041 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN A 200 " pdb=" C ASN A 200 " pdb=" N GLU A 201 " pdb=" CA GLU A 201 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL A 567 " pdb=" C VAL A 567 " pdb=" N GLN A 568 " pdb=" CA GLN A 568 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2692 0.040 - 0.080: 710 0.080 - 0.121: 309 0.121 - 0.161: 26 0.161 - 0.201: 2 Chirality restraints: 3739 Sorted by residual: chirality pdb=" CA PRO A 481 " pdb=" N PRO A 481 " pdb=" C PRO A 481 " pdb=" CB PRO A 481 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR B 519 " pdb=" N THR B 519 " pdb=" C THR B 519 " pdb=" CB THR B 519 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ILE B 211 " pdb=" N ILE B 211 " pdb=" C ILE B 211 " pdb=" CB ILE B 211 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3736 not shown) Planarity restraints: 4328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 480 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 481 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 498 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 499 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 480 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ALA A 480 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA A 480 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO A 481 " 0.008 2.00e-02 2.50e+03 ... (remaining 4325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2780 2.75 - 3.29: 24897 3.29 - 3.82: 40577 3.82 - 4.36: 50258 4.36 - 4.90: 84813 Nonbonded interactions: 203325 Sorted by model distance: nonbonded pdb=" O LEU B 193 " pdb=" OG SER B 196 " model vdw 2.212 3.040 nonbonded pdb=" O PRO A1067 " pdb=" NZ LYS A1073 " model vdw 2.227 3.120 nonbonded pdb=" ND2 ASN B 302 " pdb=" OG SER B 304 " model vdw 2.236 3.120 nonbonded pdb=" O GLY A 64 " pdb=" ND2 ASN A 431 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR B 405 " pdb=" OD1 ASN B 622 " model vdw 2.238 3.040 ... (remaining 203320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.580 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: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 58.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 0.062 24666 Z= 0.118 Angle : 0.439 7.661 33469 Z= 0.236 Chirality : 0.043 0.201 3739 Planarity : 0.003 0.061 4328 Dihedral : 11.637 88.313 9081 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 3.38 % Allowed : 8.31 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2978 helix: 0.35 (0.17), residues: 897 sheet: 0.04 (0.23), residues: 519 loop : -0.74 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 920 HIS 0.003 0.001 HIS A 176 PHE 0.008 0.001 PHE B 608 TYR 0.023 0.001 TYR B 415 ARG 0.002 0.000 ARG A1143 Details of bonding type rmsd hydrogen bonds : bond 0.24982 ( 929) hydrogen bonds : angle 8.02977 ( 2556) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.50613 ( 2) covalent geometry : bond 0.00269 (24665) covalent geometry : angle 0.43875 (33467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 196 time to evaluate : 2.859 Fit side-chains REVERT: A 151 MET cc_start: 0.6325 (mtt) cc_final: 0.6059 (mtt) REVERT: A 159 GLU cc_start: 0.8519 (tt0) cc_final: 0.8184 (tt0) REVERT: A 168 ARG cc_start: 0.7961 (pmt-80) cc_final: 0.7537 (ptp-110) REVERT: A 349 GLN cc_start: 0.8497 (mt0) cc_final: 0.8285 (mt0) REVERT: A 495 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6793 (p0) REVERT: A 511 GLN cc_start: 0.6953 (mp10) cc_final: 0.6664 (mp10) REVERT: A 639 GLU cc_start: 0.8248 (pp20) cc_final: 0.7972 (mp0) REVERT: A 800 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7310 (t-90) REVERT: A 1115 ILE cc_start: 0.8231 (pt) cc_final: 0.7952 (mm) REVERT: A 1133 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7187 (p0) REVERT: B 44 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: B 131 TYR cc_start: 0.8705 (m-80) cc_final: 0.8441 (m-80) REVERT: B 153 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 251 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7638 (mm) REVERT: B 278 TYR cc_start: 0.8644 (m-80) cc_final: 0.8386 (m-10) REVERT: B 326 TYR cc_start: 0.5440 (m-10) cc_final: 0.4853 (m-10) REVERT: B 567 ASN cc_start: 0.8712 (t0) cc_final: 0.8407 (m110) REVERT: B 902 ASP cc_start: 0.8540 (p0) cc_final: 0.8319 (p0) REVERT: B 948 ASN cc_start: 0.7688 (p0) cc_final: 0.7408 (p0) REVERT: B 963 TYR cc_start: 0.8105 (t80) cc_final: 0.7838 (t80) REVERT: B 1105 ASN cc_start: 0.8763 (m110) cc_final: 0.8478 (m110) REVERT: B 1126 TYR cc_start: 0.7864 (t80) cc_final: 0.7143 (t80) REVERT: B 1139 ASP cc_start: 0.8644 (t0) cc_final: 0.8391 (t0) REVERT: C 219 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: C 242 ILE cc_start: 0.8585 (pt) cc_final: 0.8175 (mt) REVERT: C 260 ASP cc_start: 0.6401 (m-30) cc_final: 0.6127 (m-30) REVERT: C 332 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: C 626 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6887 (ptmt) outliers start: 92 outliers final: 42 residues processed: 271 average time/residue: 0.3711 time to fit residues: 161.2823 Evaluate side-chains 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 9.9990 chunk 225 optimal weight: 0.0870 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 235 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN A1196 ASN A1200 ASN A1232 HIS B 34 GLN B 311 GLN B 460 ASN B 632 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN B 689 ASN B 787 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 ASN B1050 ASN C 436 GLN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082520 restraints weight = 49978.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.080455 restraints weight = 91754.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.081557 restraints weight = 87573.578| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24666 Z= 0.165 Angle : 0.567 10.987 33469 Z= 0.304 Chirality : 0.047 0.205 3739 Planarity : 0.004 0.063 4328 Dihedral : 4.478 28.756 3209 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 0.18 % Allowed : 3.20 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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 (0.15), residues: 2978 helix: 1.25 (0.17), residues: 923 sheet: 0.00 (0.22), residues: 573 loop : -0.74 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 920 HIS 0.011 0.001 HIS A1024 PHE 0.024 0.002 PHE A 91 TYR 0.028 0.001 TYR A 738 ARG 0.004 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 929) hydrogen bonds : angle 5.19777 ( 2556) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.16806 ( 2) covalent geometry : bond 0.00382 (24665) covalent geometry : angle 0.56748 (33467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 242 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: A 349 GLN cc_start: 0.7926 (mt0) cc_final: 0.7708 (mt0) REVERT: A 1115 ILE cc_start: 0.8335 (pt) cc_final: 0.8077 (mm) REVERT: A 1236 ASN cc_start: 0.7372 (p0) cc_final: 0.7164 (p0) REVERT: B 229 MET cc_start: 0.8664 (tpp) cc_final: 0.8457 (tpp) REVERT: B 278 TYR cc_start: 0.7444 (m-80) cc_final: 0.7239 (m-10) REVERT: B 326 TYR cc_start: 0.5135 (m-10) cc_final: 0.4855 (m-10) REVERT: B 948 ASN cc_start: 0.7159 (p0) cc_final: 0.6817 (p0) REVERT: B 994 ILE cc_start: 0.8597 (mt) cc_final: 0.8351 (mm) REVERT: B 1126 TYR cc_start: 0.7284 (t80) cc_final: 0.6617 (t80) REVERT: C 215 PHE cc_start: 0.7039 (t80) cc_final: 0.6623 (t80) REVERT: C 260 ASP cc_start: 0.6596 (m-30) cc_final: 0.6387 (m-30) REVERT: C 293 GLU cc_start: 0.6394 (pm20) cc_final: 0.5959 (mp0) REVERT: C 304 ILE cc_start: 0.7228 (pt) cc_final: 0.6984 (pt) outliers start: 5 outliers final: 2 residues processed: 246 average time/residue: 0.3730 time to fit residues: 145.9686 Evaluate side-chains 157 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 46 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 288 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 706 GLN A 736 ASN A1130 GLN A1151 ASN ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.081957 restraints weight = 49915.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.079594 restraints weight = 94940.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080581 restraints weight = 86041.107| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24666 Z= 0.156 Angle : 0.527 9.837 33469 Z= 0.284 Chirality : 0.046 0.202 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.458 28.948 3209 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.14 (0.16), residues: 2978 helix: 1.53 (0.17), residues: 923 sheet: -0.04 (0.22), residues: 569 loop : -0.76 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 920 HIS 0.006 0.001 HIS A1024 PHE 0.016 0.001 PHE B 899 TYR 0.042 0.001 TYR B 153 ARG 0.005 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 929) hydrogen bonds : angle 4.80172 ( 2556) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.86920 ( 2) covalent geometry : bond 0.00363 (24665) covalent geometry : angle 0.52717 (33467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8399 (pt) cc_final: 0.8048 (mm) REVERT: B 375 GLN cc_start: 0.7972 (mp10) cc_final: 0.7312 (mt0) REVERT: B 948 ASN cc_start: 0.7119 (p0) cc_final: 0.6773 (p0) REVERT: B 1126 TYR cc_start: 0.7266 (t80) cc_final: 0.6551 (t80) REVERT: C 215 PHE cc_start: 0.6924 (t80) cc_final: 0.6519 (t80) REVERT: C 260 ASP cc_start: 0.6735 (m-30) cc_final: 0.6495 (m-30) REVERT: C 293 GLU cc_start: 0.6405 (pm20) cc_final: 0.6024 (mp0) REVERT: C 326 TRP cc_start: 0.8663 (t60) cc_final: 0.8415 (t60) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.3421 time to fit residues: 113.1751 Evaluate side-chains 150 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 220 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 264 optimal weight: 0.3980 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 640 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 GLN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081826 restraints weight = 50438.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080712 restraints weight = 81463.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081897 restraints weight = 70602.597| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24666 Z= 0.187 Angle : 0.545 9.842 33469 Z= 0.292 Chirality : 0.046 0.220 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.558 30.407 3209 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.12 (0.15), residues: 2978 helix: 1.59 (0.17), residues: 923 sheet: -0.08 (0.22), residues: 555 loop : -0.80 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 920 HIS 0.005 0.001 HIS A1024 PHE 0.017 0.001 PHE B 899 TYR 0.029 0.001 TYR A1149 ARG 0.006 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 929) hydrogen bonds : angle 4.68067 ( 2556) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.08149 ( 2) covalent geometry : bond 0.00443 (24665) covalent geometry : angle 0.54536 (33467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7799 (mtm) cc_final: 0.7597 (mtp) REVERT: A 1115 ILE cc_start: 0.8456 (pt) cc_final: 0.8071 (mm) REVERT: B 375 GLN cc_start: 0.7894 (mp10) cc_final: 0.7256 (mt0) REVERT: B 948 ASN cc_start: 0.6994 (p0) cc_final: 0.6659 (p0) REVERT: B 1126 TYR cc_start: 0.7329 (t80) cc_final: 0.6542 (t80) REVERT: C 215 PHE cc_start: 0.7041 (t80) cc_final: 0.6641 (t80) REVERT: C 293 GLU cc_start: 0.6335 (pm20) cc_final: 0.5962 (mp0) REVERT: C 304 ILE cc_start: 0.7083 (pt) cc_final: 0.6825 (pt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3439 time to fit residues: 111.7801 Evaluate side-chains 152 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 7 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 296 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1130 GLN ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 811 GLN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081602 restraints weight = 50382.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.080232 restraints weight = 87247.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081091 restraints weight = 78826.142| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24666 Z= 0.165 Angle : 0.531 10.249 33469 Z= 0.284 Chirality : 0.046 0.268 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.505 30.581 3209 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.15 (0.16), residues: 2978 helix: 1.68 (0.17), residues: 919 sheet: -0.09 (0.22), residues: 550 loop : -0.82 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1224 HIS 0.005 0.001 HIS A1024 PHE 0.041 0.001 PHE C 708 TYR 0.024 0.001 TYR B 415 ARG 0.005 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 929) hydrogen bonds : angle 4.59398 ( 2556) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.13276 ( 2) covalent geometry : bond 0.00389 (24665) covalent geometry : angle 0.53149 (33467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.7737 (p0) cc_final: 0.7495 (p0) REVERT: A 1115 ILE cc_start: 0.8463 (pt) cc_final: 0.8064 (mm) REVERT: B 375 GLN cc_start: 0.7965 (mp10) cc_final: 0.7371 (mt0) REVERT: B 664 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7782 (mtpt) REVERT: B 948 ASN cc_start: 0.7034 (p0) cc_final: 0.6657 (p0) REVERT: B 1126 TYR cc_start: 0.7404 (t80) cc_final: 0.6627 (t80) REVERT: C 215 PHE cc_start: 0.6975 (t80) cc_final: 0.6542 (t80) REVERT: C 293 GLU cc_start: 0.6372 (pm20) cc_final: 0.5989 (mp0) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3850 time to fit residues: 122.1393 Evaluate side-chains 152 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 107 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 233 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1200 ASN B 411 HIS B 443 ASN B 632 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083501 restraints weight = 49740.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082270 restraints weight = 80996.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083163 restraints weight = 69579.438| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24666 Z= 0.124 Angle : 0.516 13.836 33469 Z= 0.274 Chirality : 0.046 0.421 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.383 29.404 3209 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.27 (0.16), residues: 2978 helix: 1.78 (0.18), residues: 920 sheet: 0.04 (0.22), residues: 564 loop : -0.78 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 961 HIS 0.004 0.001 HIS A1024 PHE 0.025 0.001 PHE A 91 TYR 0.025 0.001 TYR B 415 ARG 0.006 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 929) hydrogen bonds : angle 4.45805 ( 2556) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.19167 ( 2) covalent geometry : bond 0.00285 (24665) covalent geometry : angle 0.51562 (33467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 SER cc_start: 0.8817 (t) cc_final: 0.8612 (p) REVERT: A 197 ASN cc_start: 0.7675 (p0) cc_final: 0.7472 (p0) REVERT: A 1115 ILE cc_start: 0.8488 (pt) cc_final: 0.8111 (mm) REVERT: B 375 GLN cc_start: 0.8008 (mp10) cc_final: 0.7415 (mt0) REVERT: B 791 GLU cc_start: 0.7919 (pp20) cc_final: 0.7563 (tm-30) REVERT: B 948 ASN cc_start: 0.7034 (p0) cc_final: 0.6648 (p0) REVERT: C 215 PHE cc_start: 0.6829 (t80) cc_final: 0.6467 (t80) REVERT: C 293 GLU cc_start: 0.6351 (pm20) cc_final: 0.5984 (mp0) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.3575 time to fit residues: 119.6787 Evaluate side-chains 163 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 0.7980 chunk 270 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1096 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 ASN B 4 ASN B 17 ASN B 443 ASN B 632 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081865 restraints weight = 50241.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080736 restraints weight = 82469.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.081646 restraints weight = 71233.231| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24666 Z= 0.189 Angle : 0.547 10.688 33469 Z= 0.292 Chirality : 0.047 0.329 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.512 31.088 3209 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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 (0.16), residues: 2978 helix: 1.74 (0.17), residues: 919 sheet: -0.12 (0.21), residues: 567 loop : -0.79 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1224 HIS 0.005 0.001 HIS B 411 PHE 0.019 0.001 PHE C 708 TYR 0.024 0.001 TYR B 415 ARG 0.006 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 929) hydrogen bonds : angle 4.51432 ( 2556) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.06471 ( 2) covalent geometry : bond 0.00444 (24665) covalent geometry : angle 0.54693 (33467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 SER cc_start: 0.8917 (t) cc_final: 0.8685 (p) REVERT: A 172 MET cc_start: 0.7826 (mtm) cc_final: 0.7619 (mtp) REVERT: A 1115 ILE cc_start: 0.8505 (pt) cc_final: 0.8106 (mm) REVERT: B 948 ASN cc_start: 0.7073 (p0) cc_final: 0.6704 (p0) REVERT: C 215 PHE cc_start: 0.6896 (t80) cc_final: 0.6510 (t80) REVERT: C 293 GLU cc_start: 0.6419 (pm20) cc_final: 0.6080 (mp0) REVERT: C 304 ILE cc_start: 0.7198 (pt) cc_final: 0.6991 (pt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3678 time to fit residues: 119.8759 Evaluate side-chains 157 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 93 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 252 optimal weight: 0.0170 chunk 287 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A 756 ASN A1096 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 ASN ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B1009 ASN C 552 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083835 restraints weight = 49786.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.082862 restraints weight = 78569.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.083765 restraints weight = 66265.623| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24666 Z= 0.115 Angle : 0.511 11.831 33469 Z= 0.273 Chirality : 0.045 0.334 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.351 29.223 3209 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.32 (0.16), residues: 2978 helix: 1.87 (0.18), residues: 920 sheet: 0.07 (0.22), residues: 551 loop : -0.78 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 548 HIS 0.003 0.001 HIS A1024 PHE 0.018 0.001 PHE A 844 TYR 0.022 0.001 TYR B 415 ARG 0.006 0.000 ARG B 672 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 929) hydrogen bonds : angle 4.37413 ( 2556) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.25719 ( 2) covalent geometry : bond 0.00262 (24665) covalent geometry : angle 0.51069 (33467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 LYS cc_start: 0.8648 (tptt) cc_final: 0.8338 (tptm) REVERT: A 1115 ILE cc_start: 0.8494 (pt) cc_final: 0.8037 (mm) REVERT: B 791 GLU cc_start: 0.7934 (pp20) cc_final: 0.7621 (tm-30) REVERT: B 948 ASN cc_start: 0.6997 (p0) cc_final: 0.6642 (p0) REVERT: C 215 PHE cc_start: 0.6836 (t80) cc_final: 0.6596 (t80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3471 time to fit residues: 119.2997 Evaluate side-chains 161 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 67 optimal weight: 0.6980 chunk 230 optimal weight: 0.2980 chunk 183 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 265 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1096 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 992 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.084663 restraints weight = 50068.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.083742 restraints weight = 75762.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.084778 restraints weight = 68968.411| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24666 Z= 0.114 Angle : 0.507 11.097 33469 Z= 0.271 Chirality : 0.045 0.382 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.277 28.297 3209 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.38 (0.16), residues: 2978 helix: 1.93 (0.18), residues: 919 sheet: 0.11 (0.22), residues: 546 loop : -0.75 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1224 HIS 0.004 0.001 HIS C 199 PHE 0.017 0.001 PHE C 215 TYR 0.026 0.001 TYR B 415 ARG 0.007 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 929) hydrogen bonds : angle 4.28947 ( 2556) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.18635 ( 2) covalent geometry : bond 0.00258 (24665) covalent geometry : angle 0.50728 (33467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7256 (mmm) cc_final: 0.6994 (mpp) REVERT: A 1115 ILE cc_start: 0.8500 (pt) cc_final: 0.7968 (mm) REVERT: B 791 GLU cc_start: 0.7906 (pp20) cc_final: 0.7604 (tm-30) REVERT: B 948 ASN cc_start: 0.6952 (p0) cc_final: 0.6596 (p0) REVERT: C 407 ASN cc_start: 0.7063 (p0) cc_final: 0.6818 (m-40) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.3388 time to fit residues: 115.6448 Evaluate side-chains 162 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 276 optimal weight: 0.0010 chunk 167 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 274 ASN A 706 GLN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 992 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.080389 restraints weight = 50577.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.079080 restraints weight = 87061.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.080140 restraints weight = 76316.806| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 24666 Z= 0.282 Angle : 0.633 12.703 33469 Z= 0.336 Chirality : 0.050 0.436 3739 Planarity : 0.004 0.063 4328 Dihedral : 4.796 33.413 3209 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.14 % Favored : 94.73 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.03 (0.16), residues: 2978 helix: 1.61 (0.17), residues: 918 sheet: -0.27 (0.22), residues: 573 loop : -0.86 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 920 HIS 0.007 0.001 HIS A1024 PHE 0.020 0.002 PHE B 748 TYR 0.022 0.002 TYR B 415 ARG 0.007 0.001 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 929) hydrogen bonds : angle 4.61388 ( 2556) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.26425 ( 2) covalent geometry : bond 0.00667 (24665) covalent geometry : angle 0.63330 (33467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 LYS cc_start: 0.8707 (tptt) cc_final: 0.8395 (tptm) REVERT: A 1115 ILE cc_start: 0.8570 (pt) cc_final: 0.8141 (mm) REVERT: A 1171 LYS cc_start: 0.8206 (tptm) cc_final: 0.7718 (tptp) REVERT: A 1229 MET cc_start: 0.3308 (tpp) cc_final: 0.2720 (tpp) REVERT: C 304 ILE cc_start: 0.7277 (pt) cc_final: 0.7036 (pt) REVERT: C 522 ASN cc_start: 0.4802 (m-40) cc_final: 0.4103 (t0) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3679 time to fit residues: 108.0653 Evaluate side-chains 142 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 271 optimal weight: 30.0000 chunk 199 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1133 ASN ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 865 ASN B 992 ASN B1108 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.082144 restraints weight = 50076.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080977 restraints weight = 82915.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082066 restraints weight = 70934.921| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24666 Z= 0.167 Angle : 0.549 10.902 33469 Z= 0.294 Chirality : 0.047 0.362 3739 Planarity : 0.003 0.063 4328 Dihedral : 4.607 31.914 3209 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.11 % Allowed : 0.40 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.12 (0.16), residues: 2978 helix: 1.72 (0.17), residues: 918 sheet: -0.14 (0.22), residues: 564 loop : -0.87 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1224 HIS 0.004 0.001 HIS A1024 PHE 0.016 0.001 PHE A 636 TYR 0.022 0.001 TYR B 415 ARG 0.007 0.000 ARG A 783 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 929) hydrogen bonds : angle 4.46997 ( 2556) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.18228 ( 2) covalent geometry : bond 0.00393 (24665) covalent geometry : angle 0.54916 (33467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7047.37 seconds wall clock time: 125 minutes 43.61 seconds (7543.61 seconds total)