Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 05:25:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/04_2023/7usl_26738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/04_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_26738/04_2023/7usl_26738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/04_2023/7usl_26738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/04_2023/7usl_26738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usl_26738/04_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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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: 10.50, per 1000 atoms: 0.55 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: 7.61 Conformation dependent library (CDL) restraints added in 3.1 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: 1.75 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: 11.10 Time building geometry restraints manager: 8.25 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=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG A1212 " pdb=" O5 NAG A1212 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG A1211 " pdb=" O5 NAG A1211 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG A1206 " pdb=" O5 NAG A1206 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 ... (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: 10488 17.85 - 35.71: 790 35.71 - 53.56: 163 53.56 - 71.42: 38 71.42 - 89.27: 23 Dihedral angle restraints: 11502 sinusoidal: 4575 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 11499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1814 0.034 - 0.068: 727 0.068 - 0.102: 256 0.102 - 0.136: 128 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 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 9.690 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 55.910 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.004 0.055 19369 Z= 0.240 Angle : 0.611 8.291 26229 Z= 0.319 Chirality : 0.046 0.170 2937 Planarity : 0.004 0.072 3481 Dihedral : 13.676 89.274 6991 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 : 2.072 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: 1.4279 time to fit residues: 671.1010 Evaluate side-chains 394 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.2726 time to fit residues: 3.9810 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.0963 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= 0.225 Angle : 0.606 10.304 26229 Z= 0.317 Chirality : 0.045 0.190 2937 Planarity : 0.004 0.057 3481 Dihedral : 4.969 24.858 2659 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -0.40 (0.17), residues: 2444 helix: 0.10 (0.40), residues: 174 sheet: 0.45 (0.17), residues: 1017 loop : -0.90 (0.16), residues: 1253 *********************** 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: 39 poor density : 408 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 418 average time/residue: 1.4589 time to fit residues: 679.5269 Evaluate side-chains 393 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 376 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 5 residues processed: 13 average time/residue: 0.5323 time to fit residues: 11.7634 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 61 optimal weight: 0.0040 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 741 GLN A 858 ASN B 292 ASN B 591 GLN C1253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19369 Z= 0.174 Angle : 0.564 8.656 26229 Z= 0.295 Chirality : 0.044 0.161 2937 Planarity : 0.004 0.049 3481 Dihedral : 4.769 23.663 2659 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.10 % 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: 0.15 (0.40), residues: 175 sheet: 0.52 (0.16), residues: 1004 loop : -0.95 (0.16), residues: 1265 *********************** 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 434 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 391 time to evaluate : 2.215 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 405 average time/residue: 1.4759 time to fit residues: 668.4743 Evaluate side-chains 409 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 386 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 8 residues processed: 17 average time/residue: 0.5662 time to fit residues: 15.1278 ------------------------------------------------------------------------------- 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: 6.9990 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 0.0770 chunk 222 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- 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 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C1123 ASN C1253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 19369 Z= 0.352 Angle : 0.646 10.160 26229 Z= 0.334 Chirality : 0.047 0.185 2937 Planarity : 0.005 0.062 3481 Dihedral : 5.092 28.309 2659 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 3.32 % 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: -0.57 (0.16), residues: 2444 helix: 0.11 (0.40), residues: 174 sheet: 0.38 (0.16), residues: 1007 loop : -1.07 (0.16), residues: 1263 *********************** 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 474 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 406 time to evaluate : 2.237 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 42 residues processed: 435 average time/residue: 1.4035 time to fit residues: 683.2395 Evaluate side-chains 428 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 386 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 18 residues processed: 25 average time/residue: 0.6268 time to fit residues: 22.5885 ------------------------------------------------------------------------------- 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: 6.9990 chunk 133 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 175 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 494 GLN B 591 GLN C 776 GLN C1123 ASN C1253 ASN H 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19369 Z= 0.241 Angle : 0.605 11.743 26229 Z= 0.312 Chirality : 0.045 0.173 2937 Planarity : 0.004 0.056 3481 Dihedral : 4.971 25.938 2659 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.97 % 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: -0.53 (0.16), residues: 2444 helix: 0.14 (0.41), residues: 175 sheet: 0.42 (0.16), residues: 1001 loop : -1.06 (0.16), residues: 1268 *********************** 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 457 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 396 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 39 residues processed: 424 average time/residue: 1.4536 time to fit residues: 695.6905 Evaluate side-chains 429 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 390 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 19 residues processed: 22 average time/residue: 0.4740 time to fit residues: 17.6795 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS B 591 GLN C1253 ASN H 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 19369 Z= 0.318 Angle : 0.644 11.037 26229 Z= 0.331 Chirality : 0.047 0.186 2937 Planarity : 0.005 0.057 3481 Dihedral : 5.098 28.105 2659 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 3.32 % 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: -0.62 (0.17), residues: 2444 helix: 0.01 (0.40), residues: 181 sheet: 0.30 (0.17), residues: 1008 loop : -1.07 (0.16), residues: 1255 *********************** 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 467 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 399 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 43 residues processed: 434 average time/residue: 1.4268 time to fit residues: 694.9148 Evaluate side-chains 433 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 390 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 23 residues processed: 21 average time/residue: 0.5594 time to fit residues: 18.2059 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.0170 chunk 235 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS A 940 GLN B 332 HIS B 591 GLN C1253 ASN H 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19369 Z= 0.216 Angle : 0.614 10.590 26229 Z= 0.314 Chirality : 0.045 0.155 2937 Planarity : 0.004 0.056 3481 Dihedral : 4.928 25.902 2659 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -0.55 (0.17), residues: 2444 helix: 0.14 (0.40), residues: 181 sheet: 0.38 (0.17), residues: 1007 loop : -1.06 (0.16), residues: 1256 *********************** 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 453 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 394 time to evaluate : 2.448 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 428 average time/residue: 1.4355 time to fit residues: 688.6557 Evaluate side-chains 429 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 388 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 25 residues processed: 17 average time/residue: 0.5168 time to fit residues: 14.6858 ------------------------------------------------------------------------------- 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: 0.9980 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 160 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS B 332 HIS B 591 GLN C1253 ASN H 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19369 Z= 0.213 Angle : 0.616 10.493 26229 Z= 0.315 Chirality : 0.045 0.158 2937 Planarity : 0.004 0.064 3481 Dihedral : 4.849 25.173 2659 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.34 % 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: -0.54 (0.17), residues: 2444 helix: 0.09 (0.40), residues: 181 sheet: 0.41 (0.17), residues: 1005 loop : -1.06 (0.16), residues: 1258 *********************** 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 444 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 396 time to evaluate : 2.309 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 34 residues processed: 424 average time/residue: 1.4060 time to fit residues: 670.7963 Evaluate side-chains 417 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 383 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 8 average time/residue: 0.8510 time to fit residues: 11.3143 ------------------------------------------------------------------------------- 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: 2.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS B 332 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1253 ASN H 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 19369 Z= 0.436 Angle : 0.728 11.813 26229 Z= 0.373 Chirality : 0.050 0.200 2937 Planarity : 0.005 0.074 3481 Dihedral : 5.308 31.896 2659 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 2.83 % 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: -0.78 (0.16), residues: 2444 helix: -0.00 (0.41), residues: 174 sheet: 0.19 (0.16), residues: 1007 loop : -1.19 (0.16), residues: 1263 *********************** 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 459 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 401 time to evaluate : 2.141 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 44 residues processed: 432 average time/residue: 1.4292 time to fit residues: 692.5070 Evaluate side-chains 438 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 394 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 27 residues processed: 17 average time/residue: 0.5595 time to fit residues: 15.3746 ------------------------------------------------------------------------------- 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: 0.9990 chunk 231 optimal weight: 0.0870 chunk 141 optimal weight: 0.0980 chunk 109 optimal weight: 0.2980 chunk 161 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 49 GLN A 741 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS B 332 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1253 ASN H 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1844 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= 0.186 Angle : 0.634 11.360 26229 Z= 0.323 Chirality : 0.045 0.156 2937 Planarity : 0.005 0.071 3481 Dihedral : 4.891 24.959 2659 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.71 % 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: -0.59 (0.17), residues: 2444 helix: 0.16 (0.41), residues: 175 sheet: 0.40 (0.17), residues: 993 loop : -1.12 (0.16), residues: 1276 ********************** 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 418 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 383 time to evaluate : 2.232 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 30 residues processed: 410 average time/residue: 1.4324 time to fit residues: 660.4158 Evaluate side-chains 401 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 371 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.8023 time to fit residues: 7.8519 ------------------------------------------------------------------------------- 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: 0.9980 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 49 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN H 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.168029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145931 restraints weight = 27190.605| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.83 r_work: 0.3680 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 19369 Z= 0.378 Angle : 0.706 12.690 26229 Z= 0.360 Chirality : 0.048 0.196 2937 Planarity : 0.005 0.079 3481 Dihedral : 5.207 29.214 2659 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: -0.76 (0.16), residues: 2444 helix: 0.03 (0.40), residues: 175 sheet: 0.25 (0.17), residues: 1007 loop : -1.22 (0.16), residues: 1262 =============================================================================== Job complete usr+sys time: 9982.68 seconds wall clock time: 176 minutes 2.29 seconds (10562.29 seconds total)