Starting phenix.real_space_refine on Fri Jun 28 18:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/06_2024/7x8a_33056.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 33 5.49 5 S 57 5.16 5 C 10097 2.51 5 N 2777 2.21 5 O 3063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 1002": "OE1" <-> "OE2" Residue "A GLU 1525": "OE1" <-> "OE2" Residue "A GLU 1600": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16031 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5383 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 9955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9955 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 59, 'TRANS': 1206} Chain breaks: 5 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 1, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 12} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9001 SG CYS A 491 52.924 49.410 50.088 1.00 54.25 S ATOM 9069 SG CYS A 501 53.132 48.423 46.625 1.00 45.05 S ATOM 9083 SG CYS A 503 56.226 47.890 48.697 1.00 47.02 S ATOM 9105 SG CYS A 506 53.216 45.695 49.411 1.00 43.57 S ATOM 6059 SG CYS A 88 47.366 26.287 26.370 1.00 57.57 S ATOM 6330 SG CYS A 121 45.755 23.307 24.620 1.00 73.51 S ATOM 6376 SG CYS A 127 47.125 22.928 28.159 1.00 58.23 S ATOM 6400 SG CYS A 130 44.045 25.067 27.546 1.00 54.37 S ATOM 11073 SG CYS A 750 51.876 68.818 73.320 1.00 63.04 S ATOM 11086 SG CYS A 752 55.166 67.698 74.823 1.00 55.30 S ATOM 11108 SG CYS A 755 52.627 65.047 73.859 1.00 51.37 S ATOM 13050 SG CYS A1018 45.696 69.639 109.917 1.00 86.14 S ATOM 13231 SG CYS A1406 44.656 70.310 106.196 1.00 80.54 S ATOM 13282 SG CYS A1414 46.420 72.804 108.261 1.00 74.48 S ATOM 13299 SG CYS A1417 48.199 69.432 107.109 1.00 66.41 S Time building chain proxies: 9.11, per 1000 atoms: 0.57 Number of scatterers: 16031 At special positions: 0 Unit cell: (98.7999, 99.7499, 156.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 33 15.00 O 3063 8.00 N 2777 7.00 C 10097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 21 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 41.5% alpha, 17.4% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'D' and resid 15 through 32 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.865A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.634A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.706A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.267A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 219 " --> pdb=" O HIS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 230 through 246 removed outlier: 3.962A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.704A pdb=" N ILE D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 302 through 321 removed outlier: 4.432A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.890A pdb=" N ASP D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 361 removed outlier: 4.102A pdb=" N TYR D 360 " --> pdb=" O TYR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 451 removed outlier: 3.870A pdb=" N LEU D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 490 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.569A pdb=" N SER D 500 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.501A pdb=" N LEU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 614 removed outlier: 3.612A pdb=" N LEU D 611 " --> pdb=" O TYR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 652 removed outlier: 4.054A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 4.004A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 692 removed outlier: 3.675A pdb=" N GLU D 690 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 692 " --> pdb=" O GLN D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.674A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.530A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.940A pdb=" N ASP A 324 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.721A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 617 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.528A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.465A pdb=" N GLN A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.993A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1498 removed outlier: 3.713A pdb=" N ARG A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.811A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.523A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 removed outlier: 3.779A pdb=" N LYS A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1666 removed outlier: 3.803A pdb=" N LEU A1666 " --> pdb=" O TYR A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.553A pdb=" N LYS A1679 " --> pdb=" O LYS A1675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431 removed outlier: 3.693A pdb=" N MET D 413 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN D 408 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N CYS D 516 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER D 711 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 622 " --> pdb=" O VAL D 658 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR D 660 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.819A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.206A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 191 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 178 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A 193 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 176 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TRP A 195 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER A 174 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.897A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 5.150A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 600 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 514 removed outlier: 5.150A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.197A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB4, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.558A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.813A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.813A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.532A pdb=" N ALA A 699 " --> pdb=" O ASP A 806 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB9, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AC1, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 992 removed outlier: 7.006A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A1436 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.791A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.154A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A1507 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1421 through 1422 688 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4531 1.33 - 1.45: 2869 1.45 - 1.57: 8907 1.57 - 1.69: 65 1.69 - 1.81: 80 Bond restraints: 16452 Sorted by residual: bond pdb=" CB PRO A 982 " pdb=" CG PRO A 982 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.26e+00 bond pdb=" CA ASP A1424 " pdb=" CB ASP A1424 " ideal model delta sigma weight residual 1.530 1.549 -0.018 1.69e-02 3.50e+03 1.18e+00 bond pdb=" CA VAL D 638 " pdb=" CB VAL D 638 " ideal model delta sigma weight residual 1.540 1.554 -0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C PHE D 324 " pdb=" N SER D 325 " ideal model delta sigma weight residual 1.328 1.337 -0.009 8.50e-03 1.38e+04 1.05e+00 bond pdb=" N GLY A 710 " pdb=" CA GLY A 710 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.00e+00 ... (remaining 16447 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.56: 601 106.56 - 113.42: 8896 113.42 - 120.29: 5885 120.29 - 127.15: 6743 127.15 - 134.02: 245 Bond angle restraints: 22370 Sorted by residual: angle pdb=" C ASP D 637 " pdb=" N VAL D 638 " pdb=" CA VAL D 638 " ideal model delta sigma weight residual 121.97 128.91 -6.94 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C SER D 325 " pdb=" N LEU D 326 " pdb=" CA LEU D 326 " ideal model delta sigma weight residual 120.95 127.66 -6.71 1.78e+00 3.16e-01 1.42e+01 angle pdb=" N SER D 325 " pdb=" CA SER D 325 " pdb=" C SER D 325 " ideal model delta sigma weight residual 108.65 115.52 -6.87 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C THR A1423 " pdb=" N ASP A1424 " pdb=" CA ASP A1424 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C LYS A1543 " pdb=" N ASN A1544 " pdb=" CA ASN A1544 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 ... (remaining 22365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9697 35.94 - 71.89: 174 71.89 - 107.83: 32 107.83 - 143.77: 1 143.77 - 179.71: 3 Dihedral angle restraints: 9907 sinusoidal: 4318 harmonic: 5589 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual 232.00 52.29 179.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C -15 " pdb=" C1' U C -15 " pdb=" N1 U C -15 " pdb=" C2 U C -15 " ideal model delta sinusoidal sigma weight residual -128.00 44.36 -172.36 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 44.22 -172.22 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 9904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1940 0.046 - 0.093: 391 0.093 - 0.139: 113 0.139 - 0.186: 4 0.186 - 0.232: 1 Chirality restraints: 2449 Sorted by residual: chirality pdb=" CB VAL D 638 " pdb=" CA VAL D 638 " pdb=" CG1 VAL D 638 " pdb=" CG2 VAL D 638 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1' C C 2 " pdb=" O4' C C 2 " pdb=" C2' C C 2 " pdb=" N1 C C 2 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA ASP A1424 " pdb=" N ASP A1424 " pdb=" C ASP A1424 " pdb=" CB ASP A1424 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2446 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 981 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 982 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 982 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 982 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 629 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C THR D 629 " -0.036 2.00e-02 2.50e+03 pdb=" O THR D 629 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP D 630 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 633 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 634 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 634 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 634 " 0.026 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 424 2.70 - 3.25: 15748 3.25 - 3.80: 26227 3.80 - 4.35: 35418 4.35 - 4.90: 58659 Nonbonded interactions: 136476 Sorted by model distance: nonbonded pdb=" O ILE A 531 " pdb=" O2' A C 3 " model vdw 2.145 2.440 nonbonded pdb=" OE2 GLU A 11 " pdb=" OG1 THR A 204 " model vdw 2.146 2.440 nonbonded pdb=" O PHE A 104 " pdb=" O2' G C -10 " model vdw 2.186 2.440 nonbonded pdb=" OG1 THR A 941 " pdb=" OE1 GLU A 943 " model vdw 2.201 2.440 nonbonded pdb=" O TRP D 687 " pdb=" OG1 THR D 691 " model vdw 2.209 2.440 ... (remaining 136471 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.010 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 50.890 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.056 16452 Z= 0.206 Angle : 0.531 8.054 22370 Z= 0.279 Chirality : 0.040 0.232 2449 Planarity : 0.004 0.055 2759 Dihedral : 15.005 179.712 6313 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.19), residues: 1922 helix: 1.41 (0.20), residues: 689 sheet: -0.34 (0.34), residues: 232 loop : -0.60 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 278 HIS 0.004 0.001 HIS D 215 PHE 0.026 0.001 PHE A 731 TYR 0.023 0.001 TYR A1595 ARG 0.005 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8522 (mttp) cc_final: 0.8287 (mttm) REVERT: A 145 ARG cc_start: 0.6862 (tmt170) cc_final: 0.6629 (ttp-170) REVERT: A 463 ASP cc_start: 0.7605 (t70) cc_final: 0.7117 (t0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 1.3516 time to fit residues: 275.6272 Evaluate side-chains 125 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 ASN A 7 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16452 Z= 0.188 Angle : 0.530 8.344 22370 Z= 0.278 Chirality : 0.041 0.172 2449 Planarity : 0.004 0.046 2759 Dihedral : 12.962 179.459 2602 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 1.36 % Allowed : 8.56 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1922 helix: 1.60 (0.20), residues: 701 sheet: -0.08 (0.33), residues: 239 loop : -0.60 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 278 HIS 0.003 0.001 HIS D 699 PHE 0.021 0.001 PHE A 731 TYR 0.010 0.001 TYR D 607 ARG 0.006 0.000 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8525 (mttp) cc_final: 0.8297 (mttm) REVERT: A 463 ASP cc_start: 0.7580 (t70) cc_final: 0.7043 (t0) REVERT: A 677 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 901 ASN cc_start: 0.7701 (t0) cc_final: 0.7202 (t0) outliers start: 22 outliers final: 5 residues processed: 158 average time/residue: 1.2026 time to fit residues: 212.7286 Evaluate side-chains 129 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 215 HIS D 551 GLN A 7 ASN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16452 Z= 0.280 Angle : 0.553 7.603 22370 Z= 0.288 Chirality : 0.042 0.187 2449 Planarity : 0.004 0.064 2759 Dihedral : 13.030 178.583 2602 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.93 % Favored : 93.91 % Rotamer: Outliers : 1.55 % Allowed : 11.79 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.33 (0.19), residues: 1922 helix: 1.50 (0.20), residues: 703 sheet: -0.14 (0.32), residues: 247 loop : -0.61 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 612 HIS 0.005 0.001 HIS D 404 PHE 0.023 0.002 PHE A 129 TYR 0.019 0.001 TYR A1595 ARG 0.006 0.000 ARG D 574 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8525 (mttp) cc_final: 0.8287 (mttm) REVERT: D 665 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7690 (ptp-170) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 1.2743 time to fit residues: 210.5072 Evaluate side-chains 133 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN A 269 HIS A 286 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16452 Z= 0.205 Angle : 0.525 10.023 22370 Z= 0.273 Chirality : 0.041 0.175 2449 Planarity : 0.004 0.055 2759 Dihedral : 12.987 179.774 2602 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.62 % Favored : 94.22 % Rotamer: Outliers : 1.80 % Allowed : 13.15 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1922 helix: 1.59 (0.20), residues: 706 sheet: -0.15 (0.32), residues: 247 loop : -0.59 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS D 404 PHE 0.022 0.001 PHE A1520 TYR 0.011 0.001 TYR D 607 ARG 0.008 0.000 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8494 (mttp) cc_final: 0.8264 (mttm) REVERT: D 665 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7607 (ptp-170) REVERT: A 1581 ARG cc_start: 0.7610 (ptm160) cc_final: 0.7252 (ttt180) outliers start: 29 outliers final: 11 residues processed: 151 average time/residue: 1.0828 time to fit residues: 184.9703 Evaluate side-chains 135 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 0.0970 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16452 Z= 0.279 Angle : 0.547 8.618 22370 Z= 0.284 Chirality : 0.042 0.176 2449 Planarity : 0.004 0.050 2759 Dihedral : 13.027 179.060 2602 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 1.86 % Allowed : 14.64 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.35 (0.19), residues: 1922 helix: 1.55 (0.20), residues: 705 sheet: -0.16 (0.32), residues: 245 loop : -0.62 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 PHE 0.016 0.001 PHE A 731 TYR 0.013 0.001 TYR D 607 ARG 0.006 0.000 ARG A1452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8502 (mttp) cc_final: 0.8256 (mttm) REVERT: D 166 ASP cc_start: 0.8122 (m-30) cc_final: 0.7891 (t0) REVERT: D 665 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7667 (ptp-170) REVERT: A 821 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (ttpt) REVERT: A 972 GLU cc_start: 0.7369 (tp30) cc_final: 0.6794 (tp30) REVERT: A 1525 GLU cc_start: 0.7402 (tt0) cc_final: 0.7196 (tp30) REVERT: A 1581 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7258 (ttt180) outliers start: 30 outliers final: 18 residues processed: 151 average time/residue: 1.1755 time to fit residues: 198.9211 Evaluate side-chains 144 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16452 Z= 0.208 Angle : 0.519 7.728 22370 Z= 0.271 Chirality : 0.041 0.278 2449 Planarity : 0.004 0.048 2759 Dihedral : 12.992 179.853 2602 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.17 % Rotamer: Outliers : 1.99 % Allowed : 15.63 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.46 (0.19), residues: 1922 helix: 1.66 (0.20), residues: 705 sheet: -0.07 (0.32), residues: 250 loop : -0.60 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS A1621 PHE 0.013 0.001 PHE D 491 TYR 0.012 0.001 TYR A1595 ARG 0.011 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8447 (mttp) cc_final: 0.8190 (mttm) REVERT: D 665 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7636 (ptp-170) REVERT: A 776 ASN cc_start: 0.7534 (t0) cc_final: 0.7274 (p0) REVERT: A 821 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (ttpt) REVERT: A 1581 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7217 (ttt180) outliers start: 32 outliers final: 17 residues processed: 149 average time/residue: 1.1610 time to fit residues: 194.1865 Evaluate side-chains 143 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 159 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16452 Z= 0.141 Angle : 0.502 12.941 22370 Z= 0.261 Chirality : 0.040 0.211 2449 Planarity : 0.004 0.045 2759 Dihedral : 12.896 178.719 2602 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.80 % Rotamer: Outliers : 1.61 % Allowed : 16.69 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1922 helix: 1.77 (0.20), residues: 707 sheet: 0.02 (0.32), residues: 250 loop : -0.56 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.007 0.001 HIS A 762 PHE 0.014 0.001 PHE D 491 TYR 0.011 0.001 TYR D 704 ARG 0.007 0.000 ARG D 574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 901 ASN cc_start: 0.7680 (t0) cc_final: 0.7164 (t0) REVERT: A 1581 ARG cc_start: 0.7569 (ptm160) cc_final: 0.7343 (ttt180) outliers start: 26 outliers final: 11 residues processed: 153 average time/residue: 1.0884 time to fit residues: 188.5481 Evaluate side-chains 132 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.0270 chunk 75 optimal weight: 0.0030 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 0.2448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 HIS ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16452 Z= 0.128 Angle : 0.502 11.162 22370 Z= 0.258 Chirality : 0.040 0.226 2449 Planarity : 0.004 0.044 2759 Dihedral : 12.788 178.231 2602 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 1.05 % Allowed : 17.87 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.65 (0.19), residues: 1922 helix: 1.89 (0.20), residues: 706 sheet: 0.08 (0.32), residues: 249 loop : -0.56 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.003 0.000 HIS A1621 PHE 0.014 0.001 PHE D 491 TYR 0.011 0.001 TYR D 704 ARG 0.010 0.000 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: D 166 ASP cc_start: 0.8128 (m-30) cc_final: 0.7838 (t0) REVERT: A 808 TYR cc_start: 0.8253 (t80) cc_final: 0.7942 (t80) REVERT: A 901 ASN cc_start: 0.7653 (t0) cc_final: 0.7167 (t0) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 1.0783 time to fit residues: 175.9776 Evaluate side-chains 141 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9247 > 50: distance: 23 - 28: 25.578 distance: 28 - 29: 4.687 distance: 28 - 34: 15.434 distance: 29 - 30: 31.644 distance: 29 - 32: 3.533 distance: 30 - 31: 14.207 distance: 30 - 35: 13.604 distance: 32 - 33: 5.518 distance: 33 - 34: 8.699 distance: 35 - 36: 22.225 distance: 36 - 37: 3.299 distance: 36 - 39: 27.815 distance: 37 - 38: 24.408 distance: 37 - 43: 20.542 distance: 39 - 40: 20.855 distance: 43 - 44: 17.254 distance: 44 - 45: 27.597 distance: 44 - 47: 11.661 distance: 45 - 46: 33.849 distance: 45 - 50: 40.585 distance: 47 - 48: 18.626 distance: 47 - 49: 24.745 distance: 50 - 51: 41.407 distance: 51 - 52: 44.405 distance: 51 - 54: 41.715 distance: 52 - 56: 28.557 distance: 54 - 55: 12.332 distance: 56 - 57: 49.564 distance: 57 - 58: 23.598 distance: 57 - 60: 25.226 distance: 58 - 59: 21.869 distance: 58 - 64: 19.161 distance: 60 - 61: 13.330 distance: 64 - 65: 12.620 distance: 65 - 66: 27.761 distance: 65 - 68: 33.929 distance: 66 - 67: 11.932 distance: 66 - 73: 23.822 distance: 68 - 69: 22.088 distance: 69 - 70: 6.218 distance: 70 - 71: 4.497 distance: 73 - 74: 8.168 distance: 74 - 75: 28.235 distance: 74 - 77: 11.088 distance: 75 - 76: 32.495 distance: 75 - 81: 25.450 distance: 77 - 78: 8.234 distance: 78 - 79: 7.119 distance: 78 - 80: 32.366 distance: 81 - 82: 29.346 distance: 82 - 83: 16.615 distance: 83 - 84: 47.340 distance: 83 - 85: 22.943 distance: 85 - 86: 39.227 distance: 86 - 87: 43.058 distance: 86 - 89: 18.265 distance: 87 - 88: 30.943 distance: 87 - 93: 40.788 distance: 90 - 91: 9.494 distance: 90 - 92: 46.165 distance: 94 - 95: 12.685 distance: 95 - 96: 13.588 distance: 95 - 102: 25.478