Starting phenix.real_space_refine on Mon Aug 25 01:33:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ark_43785/08_2025/9ark_43785_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ark_43785/08_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_43785/08_2025/9ark_43785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ark_43785/08_2025/9ark_43785.map" model { file = "/net/cci-nas-00/data/ceres_data/9ark_43785/08_2025/9ark_43785_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ark_43785/08_2025/9ark_43785_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'ASN:plan1': 1, 'PHE:plan': 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: 6.29, per 1000 atoms: 0.26 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.18 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: 6.08 Time building geometry restraints manager: 2.83 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: 11.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.600 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A1143 TYR 0.023 0.001 TYR B 415 PHE 0.008 0.001 PHE B 608 TRP 0.010 0.001 TRP A 920 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00269 (24665) covalent geometry : angle 0.43875 (33467) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.50613 ( 2) hydrogen bonds : bond 0.24982 ( 929) hydrogen bonds : angle 8.02977 ( 2556) *********************** 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 : 1.046 Fit side-chains REVERT: A 151 MET cc_start: 0.6325 (mtt) cc_final: 0.6060 (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: 0.4852 (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: 0.1748 time to fit residues: 75.6213 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 : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** A 902 GLN A1096 ASN A1196 ASN A1200 ASN 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083865 restraints weight = 49738.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.081632 restraints weight = 92032.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.082710 restraints weight = 78425.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.083011 restraints weight = 54917.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083316 restraints weight = 50276.211| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24666 Z= 0.131 Angle : 0.550 11.023 33469 Z= 0.296 Chirality : 0.046 0.204 3739 Planarity : 0.004 0.063 4328 Dihedral : 4.377 27.578 3209 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 0.18 % Allowed : 3.05 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 2978 helix: 1.30 (0.17), residues: 922 sheet: 0.03 (0.22), residues: 572 loop : -0.73 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 672 TYR 0.030 0.001 TYR A 738 PHE 0.027 0.001 PHE A 91 TRP 0.010 0.001 TRP C 218 HIS 0.010 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00289 (24665) covalent geometry : angle 0.54970 (33467) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.14776 ( 2) hydrogen bonds : bond 0.04683 ( 929) hydrogen bonds : angle 5.18750 ( 2556) *********************** 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 262 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLN cc_start: 0.7920 (mt0) cc_final: 0.7690 (mt0) REVERT: A 1115 ILE cc_start: 0.8322 (pt) cc_final: 0.8053 (mm) REVERT: B 229 MET cc_start: 0.8627 (tpp) cc_final: 0.8417 (tpp) REVERT: B 278 TYR cc_start: 0.7387 (m-80) cc_final: 0.7183 (m-10) REVERT: B 326 TYR cc_start: 0.5184 (m-10) cc_final: 0.4919 (m-10) REVERT: B 948 ASN cc_start: 0.7185 (p0) cc_final: 0.6802 (p0) REVERT: B 994 ILE cc_start: 0.8599 (mt) cc_final: 0.8379 (mm) REVERT: B 1126 TYR cc_start: 0.7243 (t80) cc_final: 0.6567 (t80) REVERT: C 215 PHE cc_start: 0.6947 (t80) cc_final: 0.6552 (t80) REVERT: C 293 GLU cc_start: 0.6376 (pm20) cc_final: 0.6148 (mp0) REVERT: C 304 ILE cc_start: 0.7229 (pt) cc_final: 0.6989 (pt) outliers start: 5 outliers final: 1 residues processed: 261 average time/residue: 0.1720 time to fit residues: 71.9165 Evaluate side-chains 157 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 115 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 180 optimal weight: 0.0870 chunk 207 optimal weight: 0.0670 chunk 102 optimal weight: 0.0370 chunk 227 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A 736 ASN A 902 GLN A1130 GLN A1151 ASN A1200 ASN B 411 HIS B 632 ASN B 640 GLN B 811 GLN B 992 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.085025 restraints weight = 49958.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083970 restraints weight = 77516.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.084947 restraints weight = 67546.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.084831 restraints weight = 50684.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.085004 restraints weight = 47795.099| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 24666 Z= 0.104 Angle : 0.492 10.032 33469 Z= 0.265 Chirality : 0.045 0.196 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.196 25.967 3209 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.16), residues: 2978 helix: 1.63 (0.18), residues: 927 sheet: 0.00 (0.22), residues: 569 loop : -0.70 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 672 TYR 0.032 0.001 TYR B 469 PHE 0.014 0.001 PHE B 774 TRP 0.009 0.001 TRP A1224 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00222 (24665) covalent geometry : angle 0.49220 (33467) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.67644 ( 2) hydrogen bonds : bond 0.03825 ( 929) hydrogen bonds : angle 4.67405 ( 2556) *********************** 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 233 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLN cc_start: 0.7941 (mt0) cc_final: 0.7733 (mt0) REVERT: A 1115 ILE cc_start: 0.8460 (pt) cc_final: 0.8045 (mm) REVERT: B 375 GLN cc_start: 0.7941 (mp10) cc_final: 0.7304 (mt0) REVERT: B 948 ASN cc_start: 0.7040 (p0) cc_final: 0.6705 (p0) REVERT: B 1126 TYR cc_start: 0.7220 (t80) cc_final: 0.6545 (t80) REVERT: C 215 PHE cc_start: 0.6922 (t80) cc_final: 0.6608 (t80) REVERT: C 293 GLU cc_start: 0.6311 (pm20) cc_final: 0.5898 (mp0) REVERT: C 326 TRP cc_start: 0.8630 (t60) cc_final: 0.8388 (t60) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.1691 time to fit residues: 64.0496 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 : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 263 optimal weight: 20.0000 chunk 88 optimal weight: 0.0970 chunk 237 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 141 GLN A 376 ASN A 706 GLN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN B 632 ASN B 754 ASN B 953 ASN B 992 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082914 restraints weight = 50110.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081789 restraints weight = 82200.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.082702 restraints weight = 69839.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082622 restraints weight = 49948.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082788 restraints weight = 46461.227| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2037 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= 0.161 Angle : 0.525 9.794 33469 Z= 0.280 Chirality : 0.046 0.221 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.339 27.598 3209 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.16), residues: 2978 helix: 1.75 (0.18), residues: 920 sheet: 0.12 (0.22), residues: 547 loop : -0.74 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.037 0.001 TYR B 153 PHE 0.013 0.001 PHE B 774 TRP 0.010 0.001 TRP A 920 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00379 (24665) covalent geometry : angle 0.52504 (33467) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.09569 ( 2) hydrogen bonds : bond 0.03800 ( 929) hydrogen bonds : angle 4.59508 ( 2556) *********************** 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 208 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.7725 (p0) cc_final: 0.7416 (p0) REVERT: A 1115 ILE cc_start: 0.8489 (pt) cc_final: 0.8050 (mm) REVERT: B 375 GLN cc_start: 0.8003 (mp10) cc_final: 0.7398 (mt0) REVERT: B 948 ASN cc_start: 0.7040 (p0) cc_final: 0.6694 (p0) REVERT: B 1126 TYR cc_start: 0.7312 (t80) cc_final: 0.6637 (t80) REVERT: C 215 PHE cc_start: 0.6935 (t80) cc_final: 0.6557 (t80) REVERT: C 293 GLU cc_start: 0.6337 (pm20) cc_final: 0.5956 (mp0) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1680 time to fit residues: 56.8632 Evaluate side-chains 159 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 178 optimal weight: 0.2980 chunk 258 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 280 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 706 GLN A1130 GLN A1151 ASN B 632 ASN C 481 ASN C 488 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 = 0.3485 r_free = 0.3485 target = 0.110348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083991 restraints weight = 49753.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.083057 restraints weight = 75223.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083755 restraints weight = 71281.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083584 restraints weight = 50342.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.083627 restraints weight = 48760.872| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2166 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= 0.131 Angle : 0.511 9.947 33469 Z= 0.273 Chirality : 0.045 0.199 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.282 27.540 3209 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.16), residues: 2978 helix: 1.78 (0.18), residues: 920 sheet: 0.15 (0.22), residues: 542 loop : -0.75 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 672 TYR 0.030 0.001 TYR B 153 PHE 0.039 0.001 PHE C 708 TRP 0.011 0.001 TRP A1224 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00303 (24665) covalent geometry : angle 0.51126 (33467) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.06701 ( 2) hydrogen bonds : bond 0.03543 ( 929) hydrogen bonds : angle 4.50313 ( 2556) *********************** 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 205 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 SER cc_start: 0.8873 (t) cc_final: 0.8615 (p) REVERT: A 1115 ILE cc_start: 0.8527 (pt) cc_final: 0.8059 (mm) REVERT: B 375 GLN cc_start: 0.7981 (mp10) cc_final: 0.7404 (mt0) REVERT: B 948 ASN cc_start: 0.7052 (p0) cc_final: 0.6656 (p0) REVERT: B 1126 TYR cc_start: 0.7332 (t80) cc_final: 0.6605 (t80) REVERT: C 199 HIS cc_start: 0.7528 (t70) cc_final: 0.7311 (t70) REVERT: C 215 PHE cc_start: 0.6915 (t80) cc_final: 0.6501 (t80) REVERT: C 293 GLU cc_start: 0.6318 (pm20) cc_final: 0.5950 (mp0) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1522 time to fit residues: 50.7181 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 : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 296 optimal weight: 20.0000 chunk 73 optimal weight: 0.0980 chunk 193 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 98 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 278 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN A1130 GLN A1151 ASN B 567 ASN B 632 ASN C 436 GLN ** 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 = 0.3513 r_free = 0.3513 target = 0.112126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085778 restraints weight = 49683.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.084750 restraints weight = 75525.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085637 restraints weight = 66968.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085624 restraints weight = 49774.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085726 restraints weight = 47206.577| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24666 Z= 0.101 Angle : 0.491 10.373 33469 Z= 0.261 Chirality : 0.044 0.241 3739 Planarity : 0.003 0.065 4328 Dihedral : 4.143 26.212 3209 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2978 helix: 1.90 (0.18), residues: 920 sheet: 0.14 (0.22), residues: 556 loop : -0.75 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.021 0.001 TYR A1149 PHE 0.023 0.001 PHE C 708 TRP 0.009 0.001 TRP A 961 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00223 (24665) covalent geometry : angle 0.49101 (33467) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.13563 ( 2) hydrogen bonds : bond 0.03251 ( 929) hydrogen bonds : angle 4.35326 ( 2556) *********************** 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 223 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 211 MET cc_start: 0.7549 (mtm) cc_final: 0.7318 (mtm) REVERT: A 1115 ILE cc_start: 0.8513 (pt) cc_final: 0.8007 (mm) REVERT: B 375 GLN cc_start: 0.7925 (mp10) cc_final: 0.7347 (mt0) REVERT: B 791 GLU cc_start: 0.7901 (pp20) cc_final: 0.7589 (tm-30) REVERT: B 948 ASN cc_start: 0.6944 (p0) cc_final: 0.6616 (p0) REVERT: B 1126 TYR cc_start: 0.7274 (t80) cc_final: 0.6560 (t80) REVERT: C 215 PHE cc_start: 0.6797 (t80) cc_final: 0.6506 (t80) REVERT: C 293 GLU cc_start: 0.6301 (pm20) cc_final: 0.5936 (mp0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1505 time to fit residues: 55.2950 Evaluate side-chains 164 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 274 ASN A 706 GLN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 ASN B 632 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.109634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083082 restraints weight = 50102.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.082048 restraints weight = 77983.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083081 restraints weight = 68357.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082817 restraints weight = 47200.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.082975 restraints weight = 44754.962| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2278 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= 0.169 Angle : 0.534 10.414 33469 Z= 0.284 Chirality : 0.046 0.213 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.329 28.477 3209 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.16), residues: 2978 helix: 1.87 (0.18), residues: 920 sheet: -0.02 (0.22), residues: 553 loop : -0.74 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.025 0.001 TYR B 415 PHE 0.017 0.001 PHE C 708 TRP 0.013 0.001 TRP A1224 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00397 (24665) covalent geometry : angle 0.53442 (33467) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.13879 ( 2) hydrogen bonds : bond 0.03605 ( 929) hydrogen bonds : angle 4.42449 ( 2556) *********************** 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 208 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 720 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7145 (mt-10) REVERT: A 1115 ILE cc_start: 0.8525 (pt) cc_final: 0.7975 (mm) REVERT: B 948 ASN cc_start: 0.7087 (p0) cc_final: 0.6717 (p0) REVERT: B 1126 TYR cc_start: 0.7417 (t80) cc_final: 0.6660 (t80) REVERT: C 215 PHE cc_start: 0.6722 (t80) cc_final: 0.6443 (t80) REVERT: C 293 GLU cc_start: 0.6350 (pm20) cc_final: 0.6015 (mp0) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1495 time to fit residues: 50.3335 Evaluate side-chains 160 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 68 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 278 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 ASN B 632 ASN B 992 ASN B1009 ASN B1108 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.108964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.081229 restraints weight = 50043.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.078213 restraints weight = 84680.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079692 restraints weight = 80331.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.079859 restraints weight = 55656.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.080142 restraints weight = 45416.993| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2286 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 : 0.550 10.685 33469 Z= 0.293 Chirality : 0.047 0.325 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.471 30.045 3209 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 0.04 % Allowed : 1.10 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2978 helix: 1.77 (0.17), residues: 920 sheet: -0.15 (0.21), residues: 568 loop : -0.75 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 783 TYR 0.027 0.001 TYR B 153 PHE 0.018 0.001 PHE B 899 TRP 0.015 0.001 TRP A1224 HIS 0.005 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00445 (24665) covalent geometry : angle 0.54986 (33467) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.13088 ( 2) hydrogen bonds : bond 0.03710 ( 929) hydrogen bonds : angle 4.46556 ( 2556) *********************** 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 201 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8543 (pt) cc_final: 0.8055 (mm) REVERT: B 229 MET cc_start: 0.8845 (tpt) cc_final: 0.8563 (tpt) REVERT: B 791 GLU cc_start: 0.7952 (pp20) cc_final: 0.7603 (tm-30) REVERT: B 948 ASN cc_start: 0.7093 (p0) cc_final: 0.6704 (p0) REVERT: B 1108 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: C 215 PHE cc_start: 0.6747 (t80) cc_final: 0.6362 (t80) REVERT: C 293 GLU cc_start: 0.6495 (pm20) cc_final: 0.6130 (mp0) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1466 time to fit residues: 48.3268 Evaluate side-chains 156 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 229 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 286 optimal weight: 0.0070 chunk 147 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 706 GLN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1200 ASN B 632 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN C 552 GLN ** 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 = 0.3476 r_free = 0.3476 target = 0.109747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083035 restraints weight = 50056.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.081837 restraints weight = 81795.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083175 restraints weight = 69998.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.082896 restraints weight = 45931.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083068 restraints weight = 41848.757| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2360 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= 0.142 Angle : 0.523 10.940 33469 Z= 0.279 Chirality : 0.046 0.240 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.367 29.316 3209 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2978 helix: 1.83 (0.18), residues: 920 sheet: -0.03 (0.22), residues: 565 loop : -0.78 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 783 TYR 0.021 0.001 TYR B 153 PHE 0.025 0.001 PHE B 733 TRP 0.018 0.001 TRP C 548 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00332 (24665) covalent geometry : angle 0.52298 (33467) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.09277 ( 2) hydrogen bonds : bond 0.03521 ( 929) hydrogen bonds : angle 4.37558 ( 2556) *********************** 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 200 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8541 (pt) cc_final: 0.8010 (mm) REVERT: B 229 MET cc_start: 0.8858 (tpt) cc_final: 0.8579 (tpt) REVERT: B 375 GLN cc_start: 0.7878 (mp10) cc_final: 0.7208 (mt0) REVERT: B 791 GLU cc_start: 0.7954 (pp20) cc_final: 0.7607 (tm-30) REVERT: B 948 ASN cc_start: 0.7090 (p0) cc_final: 0.6704 (p0) REVERT: C 215 PHE cc_start: 0.6797 (t80) cc_final: 0.6537 (t80) REVERT: C 293 GLU cc_start: 0.6350 (pm20) cc_final: 0.5996 (mp0) REVERT: C 407 ASN cc_start: 0.6963 (m-40) cc_final: 0.5846 (t0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1398 time to fit residues: 46.0193 Evaluate side-chains 160 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 242 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083815 restraints weight = 50026.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.082567 restraints weight = 86085.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083777 restraints weight = 72247.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083156 restraints weight = 48476.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083537 restraints weight = 45191.530| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24666 Z= 0.140 Angle : 0.526 11.105 33469 Z= 0.280 Chirality : 0.046 0.339 3739 Planarity : 0.003 0.064 4328 Dihedral : 4.355 28.908 3209 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 2978 helix: 1.85 (0.17), residues: 920 sheet: -0.04 (0.22), residues: 564 loop : -0.76 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.025 0.001 TYR B 132 PHE 0.021 0.001 PHE B 733 TRP 0.016 0.001 TRP C 548 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00328 (24665) covalent geometry : angle 0.52555 (33467) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.09868 ( 2) hydrogen bonds : bond 0.03508 ( 929) hydrogen bonds : angle 4.34310 ( 2556) ********************** 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 202 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 706 GLN cc_start: 0.7289 (tt0) cc_final: 0.6954 (tt0) REVERT: A 1115 ILE cc_start: 0.8566 (pt) cc_final: 0.8027 (mm) REVERT: B 229 MET cc_start: 0.8842 (tpt) cc_final: 0.8565 (tpt) REVERT: B 375 GLN cc_start: 0.7881 (mp10) cc_final: 0.7182 (mt0) REVERT: B 791 GLU cc_start: 0.7950 (pp20) cc_final: 0.7624 (tm-30) REVERT: B 948 ASN cc_start: 0.7132 (p0) cc_final: 0.6763 (p0) REVERT: C 215 PHE cc_start: 0.6778 (t80) cc_final: 0.6555 (t80) REVERT: C 293 GLU cc_start: 0.6374 (pm20) cc_final: 0.6035 (mp0) REVERT: C 407 ASN cc_start: 0.7008 (m-40) cc_final: 0.6417 (t0) REVERT: C 522 ASN cc_start: 0.5130 (m-40) cc_final: 0.4320 (t0) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1397 time to fit residues: 46.4141 Evaluate side-chains 165 residues out of total 2762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 87 optimal weight: 0.0870 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 0.0270 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 193 optimal weight: 2.9990 overall best weight: 0.8618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 ASN B 17 ASN B 632 ASN ** B 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3485 r_free = 0.3485 target = 0.110259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083542 restraints weight = 49810.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.082366 restraints weight = 79348.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083520 restraints weight = 68782.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083350 restraints weight = 46797.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.083554 restraints weight = 44454.800| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24666 Z= 0.131 Angle : 0.518 11.056 33469 Z= 0.276 Chirality : 0.046 0.318 3739 Planarity : 0.003 0.063 4328 Dihedral : 4.323 28.362 3209 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.16), residues: 2978 helix: 1.88 (0.17), residues: 920 sheet: -0.01 (0.22), residues: 566 loop : -0.78 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 783 TYR 0.026 0.001 TYR A 705 PHE 0.020 0.001 PHE B 733 TRP 0.019 0.001 TRP A1224 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00304 (24665) covalent geometry : angle 0.51845 (33467) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.12369 ( 2) hydrogen bonds : bond 0.03454 ( 929) hydrogen bonds : angle 4.30284 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3460.91 seconds wall clock time: 61 minutes 16.04 seconds (3676.04 seconds total)