Starting phenix.real_space_refine (version: dev) on Sun Feb 26 04:48:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/02_2023/7usl_26738.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.015 sd= 1.362 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7985 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 4": "OD1" <-> "OD2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B ASP 361": "OD1" <-> "OD2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "C ASP 874": "OD1" <-> "OD2" Residue "C GLU 986": "OE1" <-> "OE2" Residue "C ASP 1393": "OD1" <-> "OD2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19065 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6627 Classifications: {'peptide': 856} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 816} Chain breaks: 3 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5176 Classifications: {'peptide': 673} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 637} Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5296 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 7, 'TRANS': 707} Chain breaks: 2 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 899 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 129 Unusual residues: {' CA': 3, 'NAG': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' CA': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Time building chain proxies: 10.65, per 1000 atoms: 0.56 Number of scatterers: 19065 At special positions: 0 Unit cell: (137.344, 156.658, 184.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 33 19.99 S 112 16.00 O 3806 8.00 N 3338 7.00 C 11776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1016 " distance=2.03 Simple disulfide: pdb=" SG CYS A1006 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 519 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 596 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 640 " distance=2.02 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 625 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1204 " - " ASN A 70 " " NAG A1205 " - " ASN A 680 " " NAG A1206 " - " ASN A 718 " " NAG A1207 " - " ASN A 785 " " NAG A1208 " - " ASN A 884 " " NAG A1209 " - " ASN A 924 " " NAG A1210 " - " ASN A1005 " " NAG A1211 " - " ASN A1028 " " NAG A1212 " - " ASN A1034 " " NAG B 802 " - " ASN B 190 " " NAG B 803 " - " ASN B 232 " " NAG D 1 " - " ASN A 375 " " NAG E 1 " - " ASN A1059 " Time building additional restraints: 7.85 Conformation dependent library (CDL) restraints added in 2.9 seconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 43 sheets defined 10.6% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.328A pdb=" N MET A 383 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.525A pdb=" N ASN A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.973A pdb=" N PHE A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1001 Processing helix chain 'A' and resid 1069 through 1072 removed outlier: 3.841A pdb=" N PHE A1072 " --> pdb=" O GLN A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1069 through 1072' Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.660A pdb=" N ILE B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.625A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 4.055A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.524A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.610A pdb=" N LYS B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.925A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.709A pdb=" N ARG B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 469 through 476 removed outlier: 4.051A pdb=" N ARG B 476 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.788A pdb=" N SER B 569 " --> pdb=" O VAL B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 4.108A pdb=" N GLY B 601 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.305A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 767 removed outlier: 3.759A pdb=" N MET C 759 " --> pdb=" O GLY C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 792 Processing helix chain 'C' and resid 1095 through 1103 Processing helix chain 'H' and resid 25 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.916A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.858A pdb=" N MET A 9 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 575 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR A 586 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLY A 573 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 588 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 571 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 4.075A pdb=" N GLU A 58 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.945A pdb=" N SER A 76 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 397 removed outlier: 8.966A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 416 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 431 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET A 418 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.540A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.540A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY A 472 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 512 removed outlier: 6.061A pdb=" N ASP A 521 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 553 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.792A pdb=" N GLY A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 689 removed outlier: 3.644A pdb=" N GLN A 685 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.543A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 859 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 784 " --> pdb=" O PHE A 867 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.543A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 859 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 814 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP A 868 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A 812 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 776 through 778 removed outlier: 3.501A pdb=" N ALA A 830 " --> pdb=" O SER A 849 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 776 through 778 removed outlier: 7.959A pdb=" N THR A1064 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A 907 " --> pdb=" O THR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 797 through 798 Processing sheet with id=AB8, first strand: chain 'A' and resid 912 through 915 removed outlier: 3.733A pdb=" N ARG A 933 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN A1034 " --> pdb=" O ARG A 969 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 969 " --> pdb=" O ASN A1034 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 922 through 924 removed outlier: 12.972A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 949 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE A1020 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A1010 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 922 through 924 Processing sheet with id=AC2, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.543A pdb=" N ASP B 41 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.617A pdb=" N GLN B 402 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 345 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B 378 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 76 through 77 removed outlier: 7.116A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 183 through 189 removed outlier: 7.274A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 146 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 109 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 111 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 149 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ALA B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.807A pdb=" N PHE B 442 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC8, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AC9, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 533 through 536 Processing sheet with id=AD2, first strand: chain 'B' and resid 572 through 575 removed outlier: 3.585A pdb=" N VAL B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 628 through 630 removed outlier: 6.477A pdb=" N GLN B 629 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 667 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 638 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AD5, first strand: chain 'C' and resid 776 through 779 Processing sheet with id=AD6, first strand: chain 'C' and resid 819 through 821 removed outlier: 6.076A pdb=" N TRP C 876 " --> pdb=" O ASP C 910 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 912 " --> pdb=" O TRP C 876 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 878 " --> pdb=" O ILE C 912 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 909 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP C 930 " --> pdb=" O LEU C 909 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 911 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE C 927 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU C1008 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C 929 " --> pdb=" O GLU C1008 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 838 through 839 removed outlier: 6.936A pdb=" N ILE C 887 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 920 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C1031 " --> pdb=" O VAL C1050 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C1067 " --> pdb=" O LYS C1088 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1087 " --> pdb=" O HIS C1137 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C1136 " --> pdb=" O TRP C1155 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C1154 " --> pdb=" O ARG C1173 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C1190 " --> pdb=" O ASP C1211 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C1210 " --> pdb=" O ILE C1261 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C1260 " --> pdb=" O MET C1279 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C1278 " --> pdb=" O PHE C1297 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C1296 " --> pdb=" O TYR C1315 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C1352 " --> pdb=" O VAL C1402 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C1401 " --> pdb=" O ARG C1420 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C1419 " --> pdb=" O LEU C1438 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU C1437 " --> pdb=" O TYR C1456 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 851 through 853 Processing sheet with id=AD9, first strand: chain 'C' and resid 903 through 905 removed outlier: 7.235A pdb=" N LEU C 896 " --> pdb=" O LYS C 904 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 895 " --> pdb=" O TYR C 970 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 974 " --> pdb=" O VAL C 897 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS C 992 " --> pdb=" O GLY C 973 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 990 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 978 through 979 removed outlier: 3.519A pdb=" N THR C 979 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 986 " --> pdb=" O THR C 979 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 1021 through 1023 removed outlier: 6.227A pdb=" N LEU C1040 " --> pdb=" O ILE C1059 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C1076 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG C1144 " --> pdb=" O GLY C1106 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS C1108 " --> pdb=" O ARG C1144 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C1146 " --> pdb=" O HIS C1108 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C1110 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP C1143 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG C1164 " --> pdb=" O ASP C1143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C1145 " --> pdb=" O ARG C1164 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP C1161 " --> pdb=" O THR C1180 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C1182 " --> pdb=" O ASP C1161 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C1163 " --> pdb=" O TYR C1182 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1243 " --> pdb=" O TYR C1250 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP C1252 " --> pdb=" O ARG C1241 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG C1241 " --> pdb=" O ASP C1252 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C1254 " --> pdb=" O TRP C1239 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TRP C1239 " --> pdb=" O VAL C1254 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1269 " --> pdb=" O ARG C1288 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C1287 " --> pdb=" O TYR C1306 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C1323 " --> pdb=" O ARG C1344 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C1341 " --> pdb=" O TYR C1392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.561A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.948A pdb=" N GLN H 102 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.868A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6549 1.35 - 1.47: 4527 1.47 - 1.60: 8150 1.60 - 1.72: 0 1.72 - 1.85: 143 Bond restraints: 19369 Sorted by residual: bond pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.83e+00 bond pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 1.808 1.849 -0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CG PRO A 853 " pdb=" CD PRO A 853 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.34e+00 bond pdb=" CG1 ILE C 790 " pdb=" CD1 ILE C 790 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.19e+00 bond pdb=" CG PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.42e-01 ... (remaining 19364 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 310 105.35 - 112.52: 9779 112.52 - 119.70: 6522 119.70 - 126.87: 9415 126.87 - 134.05: 203 Bond angle restraints: 26229 Sorted by residual: angle pdb=" C SER B 583 " pdb=" CA SER B 583 " pdb=" CB SER B 583 " ideal model delta sigma weight residual 116.34 110.59 5.75 1.40e+00 5.10e-01 1.69e+01 angle pdb=" N PHE C 866 " pdb=" CA PHE C 866 " pdb=" C PHE C 866 " ideal model delta sigma weight residual 113.18 117.98 -4.80 1.33e+00 5.65e-01 1.30e+01 angle pdb=" CA CYS B 537 " pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA LYS A 872 " pdb=" CB LYS A 872 " pdb=" CG LYS A 872 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C LYS C 857 " pdb=" N THR C 858 " pdb=" CA THR C 858 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 ... (remaining 26224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10587 17.85 - 35.71: 790 35.71 - 53.56: 163 53.56 - 71.42: 38 71.42 - 89.27: 23 Dihedral angle restraints: 11601 sinusoidal: 4674 harmonic: 6927 Sorted by residual: dihedral pdb=" CB CYS B 364 " pdb=" SG CYS B 364 " pdb=" SG CYS B 378 " pdb=" CB CYS B 378 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 540 " pdb=" CB CYS B 540 " ideal model delta sinusoidal sigma weight residual 93.00 162.38 -69.38 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS B 514 " pdb=" SG CYS B 514 " pdb=" SG CYS B 537 " pdb=" CB CYS B 537 " ideal model delta sinusoidal sigma weight residual 93.00 24.11 68.89 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 11598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1845 0.034 - 0.068: 712 0.068 - 0.102: 241 0.102 - 0.136: 127 0.136 - 0.170: 12 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CA THR C 858 " pdb=" N THR C 858 " pdb=" C THR C 858 " pdb=" CB THR C 858 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CG LEU C 995 " pdb=" CB LEU C 995 " pdb=" CD1 LEU C 995 " pdb=" CD2 LEU C 995 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA CYS B 537 " pdb=" N CYS B 537 " pdb=" C CYS B 537 " pdb=" CB CYS B 537 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 2934 not shown) Planarity restraints: 3494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 668 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.24e+00 pdb=" N PRO A 669 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 669 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 669 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 852 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 853 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 853 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 853 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1082 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A1083 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " 0.024 5.00e-02 4.00e+02 ... (remaining 3491 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 405 2.66 - 3.22: 17020 3.22 - 3.78: 27481 3.78 - 4.34: 39230 4.34 - 4.90: 65859 Nonbonded interactions: 149995 Sorted by model distance: nonbonded pdb=" OG SER A 402 " pdb=" O PHE A 419 " model vdw 2.106 2.440 nonbonded pdb=" OH TYR A 440 " pdb=" OD1 ASP B 250 " model vdw 2.116 2.440 nonbonded pdb=" NH1 ARG C 854 " pdb=" OE1 GLU C 868 " model vdw 2.176 2.520 nonbonded pdb=" OD2 ASP B 326 " pdb=" OG SER B 328 " model vdw 2.192 2.440 nonbonded pdb=" OG SER C 894 " pdb=" OG SER C 925 " model vdw 2.213 2.440 ... (remaining 149990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 33 9.91 5 S 112 5.16 5 C 11776 2.51 5 N 3338 2.21 5 O 3806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.030 Extract box with map and model: 9.490 Check model and map are aligned: 0.280 Process input model: 55.160 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 0.055 19369 Z= 0.224 Angle : 0.593 8.291 26229 Z= 0.315 Chirality : 0.045 0.170 2937 Planarity : 0.004 0.072 3481 Dihedral : 13.606 89.274 7090 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2444 helix: -0.29 (0.40), residues: 174 sheet: 0.39 (0.17), residues: 1020 loop : -0.89 (0.16), residues: 1250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 421 average time/residue: 1.4240 time to fit residues: 670.8346 Evaluate side-chains 394 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2674 time to fit residues: 3.8605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 overall best weight: 0.6714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 693 GLN A 741 GLN A 858 ASN B 332 HIS B 384 ASN B 494 GLN B 591 GLN C 963 GLN C1253 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19369 Z= 0.226 Angle : 0.605 10.202 26229 Z= 0.317 Chirality : 0.045 0.194 2937 Planarity : 0.004 0.056 3481 Dihedral : 5.065 24.907 2758 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2444 helix: 0.11 (0.40), residues: 174 sheet: 0.45 (0.17), residues: 1015 loop : -0.91 (0.16), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 406 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 417 average time/residue: 1.4878 time to fit residues: 691.2976 Evaluate side-chains 398 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 379 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 6 residues processed: 14 average time/residue: 0.5499 time to fit residues: 13.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 422 ASN A 693 GLN A 741 GLN A 858 ASN B 292 ASN B 332 HIS B 591 GLN C1253 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19369 Z= 0.182 Angle : 0.567 8.706 26229 Z= 0.297 Chirality : 0.045 0.163 2937 Planarity : 0.004 0.064 3481 Dihedral : 4.907 24.331 2758 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2444 helix: 0.12 (0.40), residues: 175 sheet: 0.51 (0.17), residues: 998 loop : -0.95 (0.16), residues: 1271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 394 time to evaluate : 2.251 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 409 average time/residue: 1.4978 time to fit residues: 685.2432 Evaluate side-chains 409 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 383 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 9 residues processed: 19 average time/residue: 0.6530 time to fit residues: 19.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 0.0980 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 0.0060 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 26 GLN A 858 ASN B 332 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C1123 ASN C1253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19369 Z= 0.199 Angle : 0.570 9.632 26229 Z= 0.296 Chirality : 0.045 0.167 2937 Planarity : 0.004 0.045 3481 Dihedral : 4.866 24.040 2758 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2444 helix: 0.21 (0.41), residues: 175 sheet: 0.49 (0.16), residues: 1008 loop : -1.01 (0.16), residues: 1261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 391 time to evaluate : 2.227 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 38 residues processed: 418 average time/residue: 1.4349 time to fit residues: 672.0450 Evaluate side-chains 417 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 379 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 15 residues processed: 24 average time/residue: 0.6571 time to fit residues: 22.6178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 741 GLN A 858 ASN B 494 GLN B 591 GLN C 776 GLN C1123 ASN C1253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 19369 Z= 0.249 Angle : 0.602 12.456 26229 Z= 0.311 Chirality : 0.045 0.178 2937 Planarity : 0.004 0.055 3481 Dihedral : 4.959 25.091 2758 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2444 helix: -0.00 (0.40), residues: 181 sheet: 0.45 (0.16), residues: 1013 loop : -1.03 (0.16), residues: 1250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 388 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 34 residues processed: 416 average time/residue: 1.4749 time to fit residues: 688.7285 Evaluate side-chains 423 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 389 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 17 residues processed: 17 average time/residue: 0.5763 time to fit residues: 15.8676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 0.0770 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 26 GLN A 741 GLN A 858 ASN B 332 HIS B 591 GLN H 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19369 Z= 0.203 Angle : 0.588 11.403 26229 Z= 0.303 Chirality : 0.045 0.163 2937 Planarity : 0.004 0.054 3481 Dihedral : 4.876 24.288 2758 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2444 helix: 0.15 (0.40), residues: 181 sheet: 0.44 (0.16), residues: 1015 loop : -0.99 (0.16), residues: 1248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 391 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 423 average time/residue: 1.4297 time to fit residues: 678.3799 Evaluate side-chains 419 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 383 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 24 residues processed: 12 average time/residue: 0.6260 time to fit residues: 12.4977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.0870 chunk 26 optimal weight: 0.0370 chunk 134 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 858 ASN ** A 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 591 GLN H 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19369 Z= 0.193 Angle : 0.586 11.060 26229 Z= 0.302 Chirality : 0.044 0.153 2937 Planarity : 0.004 0.053 3481 Dihedral : 4.806 24.133 2758 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2444 helix: 0.27 (0.41), residues: 181 sheet: 0.44 (0.17), residues: 1019 loop : -0.96 (0.17), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 390 time to evaluate : 2.226 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 38 residues processed: 423 average time/residue: 1.4278 time to fit residues: 678.0749 Evaluate side-chains 422 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 384 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 13 average time/residue: 0.6028 time to fit residues: 13.1670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 0.0370 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 26 GLN A 858 ASN A 916 HIS B 332 HIS B 591 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1192 GLN H 96 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19369 Z= 0.217 Angle : 0.599 10.855 26229 Z= 0.308 Chirality : 0.045 0.165 2937 Planarity : 0.004 0.059 3481 Dihedral : 4.849 24.419 2758 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2444 helix: 0.19 (0.41), residues: 181 sheet: 0.44 (0.16), residues: 1017 loop : -0.96 (0.17), residues: 1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 389 time to evaluate : 2.255 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 36 residues processed: 418 average time/residue: 1.4040 time to fit residues: 661.3846 Evaluate side-chains 415 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 379 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 26 residues processed: 11 average time/residue: 0.5675 time to fit residues: 11.5751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 26 GLN A 858 ASN A 916 HIS B 332 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN H 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 19369 Z= 0.455 Angle : 0.716 11.550 26229 Z= 0.370 Chirality : 0.050 0.205 2937 Planarity : 0.005 0.070 3481 Dihedral : 5.330 30.637 2758 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2444 helix: -0.06 (0.40), residues: 180 sheet: 0.28 (0.16), residues: 1002 loop : -1.10 (0.16), residues: 1262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 395 time to evaluate : 2.939 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 37 residues processed: 427 average time/residue: 1.4819 time to fit residues: 709.1742 Evaluate side-chains 425 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 388 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 12 average time/residue: 0.6289 time to fit residues: 12.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 20 GLN A 26 GLN A 741 GLN A 858 ASN A 916 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1253 ASN H 96 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19369 Z= 0.239 Angle : 0.642 11.835 26229 Z= 0.329 Chirality : 0.046 0.184 2937 Planarity : 0.005 0.063 3481 Dihedral : 5.089 26.667 2758 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2444 helix: 0.05 (0.40), residues: 181 sheet: 0.35 (0.17), residues: 1006 loop : -1.09 (0.16), residues: 1257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 383 time to evaluate : 2.232 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 30 residues processed: 411 average time/residue: 1.4517 time to fit residues: 671.5681 Evaluate side-chains 407 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 377 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 7 average time/residue: 0.5183 time to fit residues: 7.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 916 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C1000 GLN C1253 ASN H 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145341 restraints weight = 27215.528| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.96 r_work: 0.3664 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 19369 Z= 0.425 Angle : 0.724 12.277 26229 Z= 0.373 Chirality : 0.049 0.201 2937 Planarity : 0.005 0.070 3481 Dihedral : 5.411 30.489 2758 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2444 helix: -0.14 (0.40), residues: 180 sheet: 0.26 (0.16), residues: 1002 loop : -1.23 (0.16), residues: 1262 =============================================================================== Job complete usr+sys time: 9744.41 seconds wall clock time: 172 minutes 41.99 seconds (10361.99 seconds total)