Starting phenix.real_space_refine on Wed Mar 4 18:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xc7_33114/03_2026/7xc7_33114.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 50 5.49 5 S 51 5.16 5 C 9498 2.51 5 N 2636 2.21 5 O 2869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15108 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5054 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 19, 'TRANS': 629} Chain breaks: 5 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 11, 'ASP:plan': 10, 'ASN:plan1': 8, 'GLN:plan1': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 644 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 1, 'rna3p_pyr': 11} Link IDs: {'rna2p': 18, 'rna3p': 12} Chain: "J" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 418 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "A" Number of atoms: 8988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 8988 Classifications: {'peptide': 1191} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 55, 'TRANS': 1135} Chain breaks: 14 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 774 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 17, 'ASP:plan': 27, 'GLU:plan': 37, 'HIS:plan': 3, 'ARG:plan': 7, 'PHE:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 413 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 9495 SG CYS A 491 42.097 49.681 101.311 1.00 57.45 S ATOM 9563 SG CYS A 501 41.843 49.598 104.368 1.00 58.92 S ATOM 9577 SG CYS A 503 39.038 49.374 102.200 1.00 58.26 S ATOM 6742 SG CYS A 88 41.985 28.706 126.840 1.00 63.34 S ATOM 6980 SG CYS A 121 44.461 26.971 129.172 1.00 68.97 S ATOM 7011 SG CYS A 127 41.526 25.018 127.561 1.00 66.82 S ATOM 7035 SG CYS A 130 44.385 26.225 125.427 1.00 63.60 S ATOM 11436 SG CYS A 750 47.300 67.461 77.420 1.00 67.57 S ATOM 11449 SG CYS A 752 44.396 66.413 75.342 1.00 68.79 S ATOM 11471 SG CYS A 755 46.363 63.702 77.142 1.00 61.96 S ATOM 13267 SG CYS A1018 56.316 62.532 41.797 1.00 77.12 S ATOM 13413 SG CYS A1406 58.366 62.834 45.151 1.00 77.11 S ATOM 13464 SG CYS A1414 57.163 65.830 43.648 1.00 70.03 S ATOM 13481 SG CYS A1417 54.747 63.024 45.163 1.00 64.50 S Time building chain proxies: 3.28, per 1000 atoms: 0.22 Number of scatterers: 15108 At special positions: 0 Unit cell: (104.5, 94.9999, 151.05, 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 51 16.00 P 50 15.00 O 2869 8.00 N 2636 7.00 C 9498 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 436.7 milliseconds 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 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 A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 15 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 23 sheets defined 37.0% alpha, 17.2% beta 2 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'D' and resid 15 through 33 removed outlier: 3.569A pdb=" N ASN D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 41 through 58 removed outlier: 3.762A 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: 3.654A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 154 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.587A 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 209 through 224 removed outlier: 3.808A pdb=" N LYS D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.766A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 266 removed outlier: 3.531A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 298 Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.530A pdb=" N ILE D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 3.803A pdb=" N GLN D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 450 removed outlier: 3.544A pdb=" N PHE D 437 " --> pdb=" O TYR D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 removed outlier: 3.814A pdb=" N GLY D 466 " --> pdb=" O CYS D 462 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 473 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 566 through 571 removed outlier: 3.700A pdb=" N LEU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 571 " --> pdb=" O SER D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 571' Processing helix chain 'D' and resid 606 through 614 Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.554A pdb=" N GLY D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 685 through 692 removed outlier: 3.613A pdb=" N GLY D 692 " --> pdb=" O GLN D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.565A pdb=" N ARG D 705 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 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 removed outlier: 3.579A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 288 through 292 removed outlier: 5.678A pdb=" N GLU A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 292 " --> pdb=" O LYS A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 292' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.825A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 removed outlier: 3.697A pdb=" N GLU A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.527A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.666A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.551A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.996A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 873 through 880 Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.780A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.045A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.789A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1499 removed outlier: 3.822A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1590 through 1599 Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1664 through 1668 Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 432 removed outlier: 3.582A pdb=" N SER D 425 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 427 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 429 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 431 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 406 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 402 " --> pdb=" O PHE D 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 562 through 563 removed outlier: 6.007A pdb=" N LEU D 538 " --> pdb=" O LYS D 562 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 539 " --> pdb=" O THR D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 621 through 622 removed outlier: 7.738A pdb=" N VAL D 622 " --> pdb=" O VAL D 658 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR D 660 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.767A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.767A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 205 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.642A pdb=" N TRP A 82 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 85 " --> pdb=" O TRP A 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.531A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.254A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AB1, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AB2, first strand: chain 'A' and resid 512 through 513 removed outlier: 6.464A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 512 through 513 removed outlier: 6.464A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.739A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB6, first strand: chain 'A' and resid 526 through 534 removed outlier: 11.125A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.661A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.944A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.916A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.916A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.842A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 926 through 927 Processing sheet with id=AC2, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 4.134A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.977A 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: 4.134A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.307A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 991 through 992 580 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4580 1.34 - 1.46: 2731 1.46 - 1.57: 8064 1.57 - 1.69: 98 1.69 - 1.81: 68 Bond restraints: 15541 Sorted by residual: bond pdb=" CB MET D 216 " pdb=" CG MET D 216 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CB ASP A 520 " pdb=" CG ASP A 520 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CG GLU D 214 " pdb=" CD GLU D 214 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.06e+00 bond pdb=" CB ILE D 240 " pdb=" CG1 ILE D 240 " ideal model delta sigma weight residual 1.530 1.510 0.020 2.00e-02 2.50e+03 9.97e-01 bond pdb=" CA ASP A 400 " pdb=" CB ASP A 400 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.79e-01 ... (remaining 15536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 21048 2.38 - 4.77: 199 4.77 - 7.15: 22 7.15 - 9.54: 2 9.54 - 11.92: 1 Bond angle restraints: 21272 Sorted by residual: angle pdb=" C ALA A 713 " pdb=" CA ALA A 713 " pdb=" CB ALA A 713 " ideal model delta sigma weight residual 116.34 109.98 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" CB MET D 216 " pdb=" CG MET D 216 " pdb=" SD MET D 216 " ideal model delta sigma weight residual 112.70 100.78 11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C HIS A 143 " pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N ALA A 713 " pdb=" CA ALA A 713 " pdb=" C ALA A 713 " ideal model delta sigma weight residual 108.00 112.83 -4.83 1.48e+00 4.57e-01 1.06e+01 angle pdb=" C LYS D 213 " pdb=" N GLU D 214 " pdb=" CA GLU D 214 " ideal model delta sigma weight residual 120.29 115.90 4.39 1.42e+00 4.96e-01 9.54e+00 ... (remaining 21267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 9032 36.00 - 72.00: 209 72.00 - 107.99: 28 107.99 - 143.99: 0 143.99 - 179.99: 3 Dihedral angle restraints: 9272 sinusoidal: 3986 harmonic: 5286 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 -128.00 51.99 -179.99 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U J 36 " pdb=" C1' U J 36 " pdb=" N1 U J 36 " pdb=" C2 U J 36 " ideal model delta sinusoidal sigma weight residual -128.00 50.46 -178.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLN A 112 " pdb=" C GLN A 112 " pdb=" N TRP A 113 " pdb=" CA TRP A 113 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2084 0.059 - 0.118: 295 0.118 - 0.177: 24 0.177 - 0.236: 2 0.236 - 0.295: 1 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CB ILE A1468 " pdb=" CA ILE A1468 " pdb=" CG1 ILE A1468 " pdb=" CG2 ILE A1468 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 470 " pdb=" CA ILE A 470 " pdb=" CG1 ILE A 470 " pdb=" CG2 ILE A 470 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE A 965 " pdb=" CA ILE A 965 " pdb=" CG1 ILE A 965 " pdb=" CG2 ILE A 965 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 2403 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 576 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO D 577 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 577 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 577 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 700 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO D 701 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 701 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 701 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 520 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C ASP A 520 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP A 520 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 521 " 0.010 2.00e-02 2.50e+03 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 351 2.69 - 3.24: 14876 3.24 - 3.79: 24313 3.79 - 4.35: 32303 4.35 - 4.90: 52684 Nonbonded interactions: 124527 Sorted by model distance: nonbonded pdb=" O ALA D 626 " pdb=" OG1 THR D 660 " model vdw 2.134 3.040 nonbonded pdb=" OG SER D 317 " pdb=" O PHE D 405 " model vdw 2.161 3.040 nonbonded pdb=" O ASP D 217 " pdb=" OG1 THR D 220 " model vdw 2.178 3.040 nonbonded pdb=" O VAL A 735 " pdb=" OG1 THR A 739 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU A 465 " pdb=" NH2 ARG A 467 " model vdw 2.224 3.120 ... (remaining 124522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.670 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 0.039 15556 Z= 0.120 Angle : 0.589 11.923 21287 Z= 0.301 Chirality : 0.041 0.295 2406 Planarity : 0.004 0.054 2524 Dihedral : 16.028 179.991 5864 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.05 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1798 helix: 0.58 (0.21), residues: 615 sheet: -0.43 (0.34), residues: 255 loop : -1.07 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 294 TYR 0.017 0.001 TYR A 808 PHE 0.030 0.001 PHE D 254 TRP 0.027 0.002 TRP A 113 HIS 0.006 0.001 HIS D 230 Details of bonding type rmsd covalent geometry : bond 0.00259 (15541) covalent geometry : angle 0.57618 (21272) hydrogen bonds : bond 0.19473 ( 539) hydrogen bonds : angle 7.94613 ( 1657) metal coordination : bond 0.00517 ( 15) metal coordination : angle 4.65441 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6723 (mm-30) REVERT: D 202 TYR cc_start: 0.7104 (m-80) cc_final: 0.6793 (m-80) REVERT: D 230 HIS cc_start: 0.6861 (t-90) cc_final: 0.6639 (t70) REVERT: D 234 ASP cc_start: 0.6356 (m-30) cc_final: 0.6115 (m-30) REVERT: D 275 ARG cc_start: 0.6717 (mmm-85) cc_final: 0.6330 (mmm-85) REVERT: D 514 HIS cc_start: 0.7049 (m90) cc_final: 0.6745 (m90) REVERT: A 31 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6776 (mtpt) REVERT: A 236 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7377 (mtt180) REVERT: A 291 GLU cc_start: 0.6666 (tp30) cc_final: 0.6438 (tp30) REVERT: A 355 TRP cc_start: 0.7594 (t-100) cc_final: 0.7144 (t-100) REVERT: A 555 LEU cc_start: 0.8451 (mt) cc_final: 0.8231 (mt) REVERT: A 627 MET cc_start: 0.7280 (mtm) cc_final: 0.7004 (mtp) REVERT: A 630 LYS cc_start: 0.8291 (mttp) cc_final: 0.8073 (mtpp) REVERT: A 1514 LYS cc_start: 0.8215 (ttpp) cc_final: 0.8015 (ttpp) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.1394 time to fit residues: 67.1621 Evaluate side-chains 298 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN D 480 ASN A 287 ASN A 459 ASN A 668 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 HIS ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN A1592 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139727 restraints weight = 21597.026| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.22 r_work: 0.3734 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15556 Z= 0.149 Angle : 0.609 10.009 21287 Z= 0.310 Chirality : 0.043 0.245 2406 Planarity : 0.005 0.052 2524 Dihedral : 15.231 179.271 2734 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 1.81 % Allowed : 10.93 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1798 helix: 0.67 (0.21), residues: 623 sheet: -0.38 (0.35), residues: 235 loop : -1.14 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 294 TYR 0.021 0.002 TYR A1595 PHE 0.019 0.001 PHE D 239 TRP 0.020 0.001 TRP A 612 HIS 0.004 0.001 HIS A1617 Details of bonding type rmsd covalent geometry : bond 0.00330 (15541) covalent geometry : angle 0.59464 (21272) hydrogen bonds : bond 0.04836 ( 539) hydrogen bonds : angle 5.41494 ( 1657) metal coordination : bond 0.00616 ( 15) metal coordination : angle 5.04471 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 336 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 62 ASP cc_start: 0.7470 (m-30) cc_final: 0.7240 (m-30) REVERT: D 91 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6967 (mm-30) REVERT: D 148 LEU cc_start: 0.8310 (mt) cc_final: 0.8057 (mt) REVERT: D 214 GLU cc_start: 0.7259 (mp0) cc_final: 0.6777 (mp0) REVERT: D 234 ASP cc_start: 0.6862 (m-30) cc_final: 0.6616 (m-30) REVERT: D 406 TYR cc_start: 0.8412 (t80) cc_final: 0.7831 (t80) REVERT: D 437 PHE cc_start: 0.8181 (t80) cc_final: 0.7941 (t80) REVERT: D 514 HIS cc_start: 0.7675 (m90) cc_final: 0.7336 (m90) REVERT: D 541 ASN cc_start: 0.7718 (t0) cc_final: 0.7425 (t0) REVERT: A 31 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7577 (mtpt) REVERT: A 36 MET cc_start: 0.7796 (mmm) cc_final: 0.7506 (tpt) REVERT: A 168 ARG cc_start: 0.6174 (ttp80) cc_final: 0.5741 (ttp80) REVERT: A 198 ASP cc_start: 0.7300 (t0) cc_final: 0.7010 (t0) REVERT: A 355 TRP cc_start: 0.7751 (t-100) cc_final: 0.7365 (t-100) REVERT: A 415 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6962 (tm-30) REVERT: A 528 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7651 (mtp180) REVERT: A 531 ILE cc_start: 0.8686 (tp) cc_final: 0.8400 (pt) REVERT: A 630 LYS cc_start: 0.8237 (mttp) cc_final: 0.8003 (mtpp) REVERT: A 662 LYS cc_start: 0.7885 (mptt) cc_final: 0.7586 (mttm) REVERT: A 1487 TRP cc_start: 0.7585 (p-90) cc_final: 0.7158 (p-90) outliers start: 25 outliers final: 18 residues processed: 345 average time/residue: 0.1306 time to fit residues: 64.5637 Evaluate side-chains 343 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 325 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1560 VAL Chi-restraints excluded: chain A residue 1631 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 43 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 157 optimal weight: 0.0170 chunk 104 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS D 230 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 HIS D 688 GLN A 109 HIS A 276 GLN A 668 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141117 restraints weight = 21600.787| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.15 r_work: 0.3740 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15556 Z= 0.126 Angle : 0.582 9.888 21287 Z= 0.294 Chirality : 0.042 0.281 2406 Planarity : 0.004 0.051 2524 Dihedral : 15.174 179.128 2734 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 2.03 % Allowed : 14.70 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1798 helix: 0.82 (0.21), residues: 624 sheet: -0.34 (0.34), residues: 233 loop : -1.17 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 275 TYR 0.022 0.001 TYR D 259 PHE 0.015 0.001 PHE A 381 TRP 0.019 0.001 TRP A 612 HIS 0.003 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00279 (15541) covalent geometry : angle 0.56739 (21272) hydrogen bonds : bond 0.04225 ( 539) hydrogen bonds : angle 4.96876 ( 1657) metal coordination : bond 0.00510 ( 15) metal coordination : angle 4.85207 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7360 (tt0) REVERT: D 30 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 91 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6956 (mm-30) REVERT: D 148 LEU cc_start: 0.8297 (mt) cc_final: 0.8043 (mt) REVERT: D 164 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6262 (tm-30) REVERT: D 230 HIS cc_start: 0.7171 (t-90) cc_final: 0.6794 (t70) REVERT: D 234 ASP cc_start: 0.6848 (m-30) cc_final: 0.6614 (m-30) REVERT: D 353 VAL cc_start: 0.8255 (p) cc_final: 0.8016 (p) REVERT: D 405 PHE cc_start: 0.8168 (m-80) cc_final: 0.7962 (m-80) REVERT: D 406 TYR cc_start: 0.8403 (t80) cc_final: 0.7683 (t80) REVERT: D 408 ASN cc_start: 0.7347 (m-40) cc_final: 0.7102 (m-40) REVERT: D 484 VAL cc_start: 0.8437 (t) cc_final: 0.8136 (m) REVERT: D 514 HIS cc_start: 0.7655 (m90) cc_final: 0.7388 (m90) REVERT: D 541 ASN cc_start: 0.7674 (t0) cc_final: 0.7406 (t0) REVERT: D 696 TYR cc_start: 0.6880 (p90) cc_final: 0.6182 (p90) REVERT: A 23 TRP cc_start: 0.5694 (t60) cc_final: 0.5270 (t-100) REVERT: A 31 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7533 (mtpt) REVERT: A 177 ILE cc_start: 0.8048 (mt) cc_final: 0.7736 (tt) REVERT: A 198 ASP cc_start: 0.7259 (t0) cc_final: 0.6988 (t0) REVERT: A 355 TRP cc_start: 0.7672 (t-100) cc_final: 0.7267 (t-100) REVERT: A 415 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 465 GLU cc_start: 0.7670 (tt0) cc_final: 0.7461 (tt0) REVERT: A 612 TRP cc_start: 0.8057 (m-90) cc_final: 0.7634 (m-90) REVERT: A 630 LYS cc_start: 0.8222 (mttp) cc_final: 0.8002 (mtpp) outliers start: 28 outliers final: 17 residues processed: 339 average time/residue: 0.1442 time to fit residues: 69.6049 Evaluate side-chains 347 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 75 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 446 ASN D 457 HIS A 276 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.150839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138730 restraints weight = 21611.833| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.15 r_work: 0.3708 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15556 Z= 0.165 Angle : 0.609 10.049 21287 Z= 0.304 Chirality : 0.043 0.277 2406 Planarity : 0.004 0.052 2524 Dihedral : 15.208 179.433 2734 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1798 helix: 0.82 (0.21), residues: 621 sheet: -0.33 (0.35), residues: 234 loop : -1.23 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 275 TYR 0.018 0.002 TYR A 808 PHE 0.018 0.002 PHE D 254 TRP 0.021 0.001 TRP A 612 HIS 0.004 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00369 (15541) covalent geometry : angle 0.58632 (21272) hydrogen bonds : bond 0.04124 ( 539) hydrogen bonds : angle 4.80855 ( 1657) metal coordination : bond 0.00964 ( 15) metal coordination : angle 6.22762 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 336 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7319 (tp30) REVERT: D 30 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7472 (mm-30) REVERT: D 91 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7007 (mm-30) REVERT: D 210 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6174 (m-70) REVERT: D 214 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6888 (mp0) REVERT: D 230 HIS cc_start: 0.7200 (t-90) cc_final: 0.6830 (t70) REVERT: D 234 ASP cc_start: 0.6848 (m-30) cc_final: 0.6609 (m-30) REVERT: D 266 GLU cc_start: 0.5702 (tt0) cc_final: 0.4089 (tt0) REVERT: D 353 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (p) REVERT: D 405 PHE cc_start: 0.8333 (m-80) cc_final: 0.7990 (m-80) REVERT: D 541 ASN cc_start: 0.7734 (t0) cc_final: 0.7464 (t0) REVERT: D 706 SER cc_start: 0.8270 (t) cc_final: 0.7829 (p) REVERT: A 8 ILE cc_start: 0.7695 (mt) cc_final: 0.7284 (mt) REVERT: A 23 TRP cc_start: 0.5731 (t60) cc_final: 0.5311 (t-100) REVERT: A 31 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7623 (mtpt) REVERT: A 198 ASP cc_start: 0.7251 (t0) cc_final: 0.6965 (t0) REVERT: A 355 TRP cc_start: 0.7676 (t-100) cc_final: 0.7208 (t-100) REVERT: A 415 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 465 GLU cc_start: 0.7751 (tt0) cc_final: 0.7530 (tt0) REVERT: A 531 ILE cc_start: 0.8674 (tp) cc_final: 0.8471 (pt) REVERT: A 624 GLU cc_start: 0.7762 (mp0) cc_final: 0.7416 (mp0) REVERT: A 703 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8398 (ptpp) outliers start: 36 outliers final: 26 residues processed: 354 average time/residue: 0.1326 time to fit residues: 67.4036 Evaluate side-chains 357 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 329 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 23 optimal weight: 0.1980 chunk 157 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 21 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN D 480 ASN D 688 GLN A 276 GLN A 498 GLN A 616 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140113 restraints weight = 21729.977| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.14 r_work: 0.3740 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15556 Z= 0.129 Angle : 0.589 10.108 21287 Z= 0.295 Chirality : 0.042 0.326 2406 Planarity : 0.004 0.053 2524 Dihedral : 15.197 179.912 2734 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.83 % Rotamer: Outliers : 2.75 % Allowed : 17.45 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1798 helix: 0.89 (0.21), residues: 621 sheet: -0.32 (0.34), residues: 238 loop : -1.22 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 263 TYR 0.018 0.001 TYR D 259 PHE 0.016 0.001 PHE D 254 TRP 0.029 0.001 TRP A1487 HIS 0.003 0.001 HIS A1483 Details of bonding type rmsd covalent geometry : bond 0.00288 (15541) covalent geometry : angle 0.56863 (21272) hydrogen bonds : bond 0.03856 ( 539) hydrogen bonds : angle 4.68547 ( 1657) metal coordination : bond 0.00751 ( 15) metal coordination : angle 5.82372 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7314 (tp30) REVERT: D 30 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7448 (mm-30) REVERT: D 91 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6956 (mm-30) REVERT: D 148 LEU cc_start: 0.8266 (mt) cc_final: 0.8005 (mt) REVERT: D 206 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7043 (mptt) REVERT: D 207 LYS cc_start: 0.8487 (mppt) cc_final: 0.8035 (mppt) REVERT: D 210 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5973 (m-70) REVERT: D 214 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6781 (mp0) REVERT: D 230 HIS cc_start: 0.7169 (t-90) cc_final: 0.6774 (t70) REVERT: D 234 ASP cc_start: 0.6876 (m-30) cc_final: 0.6628 (m-30) REVERT: D 266 GLU cc_start: 0.5763 (tt0) cc_final: 0.3902 (tt0) REVERT: D 353 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8040 (p) REVERT: D 405 PHE cc_start: 0.8295 (m-80) cc_final: 0.7869 (m-80) REVERT: D 430 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7084 (mm-30) REVERT: D 458 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7669 (tp) REVERT: D 477 PHE cc_start: 0.7449 (t80) cc_final: 0.7062 (t80) REVERT: D 541 ASN cc_start: 0.7679 (t0) cc_final: 0.7423 (t0) REVERT: D 706 SER cc_start: 0.8215 (t) cc_final: 0.7784 (p) REVERT: A 23 TRP cc_start: 0.5717 (t60) cc_final: 0.5302 (t-100) REVERT: A 31 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7574 (mtpt) REVERT: A 198 ASP cc_start: 0.7241 (t0) cc_final: 0.6928 (t0) REVERT: A 355 TRP cc_start: 0.7665 (t-100) cc_final: 0.7178 (t-100) REVERT: A 415 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 465 GLU cc_start: 0.7742 (tt0) cc_final: 0.7520 (tt0) REVERT: A 624 GLU cc_start: 0.7740 (mp0) cc_final: 0.7373 (mp0) REVERT: A 703 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8354 (ptpp) REVERT: A 1487 TRP cc_start: 0.7648 (p-90) cc_final: 0.7428 (p-90) outliers start: 38 outliers final: 28 residues processed: 349 average time/residue: 0.1364 time to fit residues: 67.9146 Evaluate side-chains 356 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 80 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 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 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN A 616 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137304 restraints weight = 21535.610| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.17 r_work: 0.3692 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15556 Z= 0.186 Angle : 0.627 10.164 21287 Z= 0.313 Chirality : 0.043 0.316 2406 Planarity : 0.004 0.051 2524 Dihedral : 15.248 178.794 2734 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.26 % Allowed : 18.61 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1798 helix: 0.75 (0.20), residues: 623 sheet: -0.31 (0.35), residues: 237 loop : -1.27 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 275 TYR 0.020 0.002 TYR D 259 PHE 0.028 0.002 PHE D 254 TRP 0.019 0.001 TRP A 612 HIS 0.003 0.001 HIS A 942 Details of bonding type rmsd covalent geometry : bond 0.00414 (15541) covalent geometry : angle 0.60559 (21272) hydrogen bonds : bond 0.04033 ( 539) hydrogen bonds : angle 4.73235 ( 1657) metal coordination : bond 0.01162 ( 15) metal coordination : angle 6.15625 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7266 (tp30) REVERT: D 30 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 91 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7047 (mm-30) REVERT: D 148 LEU cc_start: 0.8267 (mt) cc_final: 0.8006 (mt) REVERT: D 206 LYS cc_start: 0.7415 (ptpp) cc_final: 0.7101 (mptt) REVERT: D 207 LYS cc_start: 0.8496 (mppt) cc_final: 0.8040 (mppt) REVERT: D 214 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 230 HIS cc_start: 0.7222 (t-90) cc_final: 0.6861 (t70) REVERT: D 234 ASP cc_start: 0.6864 (m-30) cc_final: 0.6622 (m-30) REVERT: D 266 GLU cc_start: 0.5950 (tt0) cc_final: 0.4339 (tt0) REVERT: D 353 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (p) REVERT: D 405 PHE cc_start: 0.8338 (m-80) cc_final: 0.7960 (m-80) REVERT: D 514 HIS cc_start: 0.7773 (m90) cc_final: 0.7535 (m90) REVERT: D 541 ASN cc_start: 0.7764 (t0) cc_final: 0.7511 (t0) REVERT: D 651 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7373 (tt) REVERT: D 706 SER cc_start: 0.8303 (t) cc_final: 0.7853 (p) REVERT: A 8 ILE cc_start: 0.7668 (mt) cc_final: 0.7330 (mt) REVERT: A 23 TRP cc_start: 0.5789 (t60) cc_final: 0.5369 (t-100) REVERT: A 62 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5476 (tp) REVERT: A 198 ASP cc_start: 0.7271 (t0) cc_final: 0.6936 (t0) REVERT: A 355 TRP cc_start: 0.7632 (t-100) cc_final: 0.7109 (t-100) REVERT: A 415 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 465 GLU cc_start: 0.7774 (tt0) cc_final: 0.7528 (tt0) REVERT: A 624 GLU cc_start: 0.7791 (mp0) cc_final: 0.7396 (mp0) REVERT: A 630 LYS cc_start: 0.8339 (mttm) cc_final: 0.8056 (mttp) REVERT: A 703 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8356 (ptpp) REVERT: A 866 ILE cc_start: 0.8429 (mt) cc_final: 0.8117 (mt) REVERT: A 1485 ASN cc_start: 0.7767 (t0) cc_final: 0.7479 (t0) REVERT: A 1512 MET cc_start: 0.7931 (mmp) cc_final: 0.7727 (mmp) outliers start: 45 outliers final: 29 residues processed: 364 average time/residue: 0.1359 time to fit residues: 70.9199 Evaluate side-chains 364 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 171 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 165 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN D 480 ASN A 39 GLN A 498 GLN A 616 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139434 restraints weight = 21539.721| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.21 r_work: 0.3727 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15556 Z= 0.136 Angle : 0.611 12.197 21287 Z= 0.305 Chirality : 0.042 0.375 2406 Planarity : 0.004 0.054 2524 Dihedral : 15.217 179.716 2734 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 2.97 % Allowed : 19.12 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1798 helix: 0.88 (0.21), residues: 622 sheet: -0.37 (0.34), residues: 238 loop : -1.26 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 120 TYR 0.024 0.001 TYR D 259 PHE 0.024 0.001 PHE D 254 TRP 0.034 0.001 TRP A1487 HIS 0.004 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00309 (15541) covalent geometry : angle 0.59312 (21272) hydrogen bonds : bond 0.03815 ( 539) hydrogen bonds : angle 4.63093 ( 1657) metal coordination : bond 0.00774 ( 15) metal coordination : angle 5.61986 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 30 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7521 (mm-30) REVERT: D 148 LEU cc_start: 0.8306 (mt) cc_final: 0.8033 (mt) REVERT: D 206 LYS cc_start: 0.7369 (ptpp) cc_final: 0.7056 (mptt) REVERT: D 207 LYS cc_start: 0.8478 (mppt) cc_final: 0.8022 (mppt) REVERT: D 214 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7085 (mt-10) REVERT: D 230 HIS cc_start: 0.7193 (t-90) cc_final: 0.6818 (t70) REVERT: D 234 ASP cc_start: 0.6885 (m-30) cc_final: 0.6635 (m-30) REVERT: D 266 GLU cc_start: 0.5758 (tt0) cc_final: 0.4007 (tt0) REVERT: D 353 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 405 PHE cc_start: 0.8316 (m-80) cc_final: 0.7854 (m-80) REVERT: D 484 VAL cc_start: 0.8453 (t) cc_final: 0.8135 (m) REVERT: D 541 ASN cc_start: 0.7720 (t0) cc_final: 0.7463 (t0) REVERT: D 651 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7356 (tt) REVERT: D 706 SER cc_start: 0.8286 (t) cc_final: 0.7830 (p) REVERT: A 23 TRP cc_start: 0.5758 (t60) cc_final: 0.5358 (t-100) REVERT: A 62 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.5347 (tp) REVERT: A 198 ASP cc_start: 0.7272 (t0) cc_final: 0.6922 (t0) REVERT: A 355 TRP cc_start: 0.7622 (t-100) cc_final: 0.7119 (t-100) REVERT: A 415 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6879 (tm-30) REVERT: A 465 GLU cc_start: 0.7751 (tt0) cc_final: 0.7509 (tt0) REVERT: A 612 TRP cc_start: 0.8074 (m-90) cc_final: 0.7761 (m-90) REVERT: A 624 GLU cc_start: 0.7795 (mp0) cc_final: 0.7364 (mp0) REVERT: A 630 LYS cc_start: 0.8294 (mttm) cc_final: 0.8018 (mttp) REVERT: A 703 LYS cc_start: 0.8618 (ptpp) cc_final: 0.8348 (ptpp) REVERT: A 835 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7261 (mtmt) REVERT: A 1485 ASN cc_start: 0.7732 (t0) cc_final: 0.7492 (t0) outliers start: 41 outliers final: 33 residues processed: 364 average time/residue: 0.1246 time to fit residues: 64.9373 Evaluate side-chains 371 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 335 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 108 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN A 276 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137789 restraints weight = 21675.804| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.11 r_work: 0.3713 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15556 Z= 0.181 Angle : 0.644 12.981 21287 Z= 0.320 Chirality : 0.044 0.374 2406 Planarity : 0.004 0.052 2524 Dihedral : 15.260 179.117 2734 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.04 % Allowed : 19.62 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1798 helix: 0.80 (0.20), residues: 623 sheet: -0.48 (0.34), residues: 240 loop : -1.32 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 120 TYR 0.020 0.002 TYR A 18 PHE 0.016 0.002 PHE A 192 TRP 0.057 0.002 TRP A1487 HIS 0.004 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00408 (15541) covalent geometry : angle 0.62437 (21272) hydrogen bonds : bond 0.03960 ( 539) hydrogen bonds : angle 4.68043 ( 1657) metal coordination : bond 0.01053 ( 15) metal coordination : angle 5.93392 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 345 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 148 LEU cc_start: 0.8330 (mt) cc_final: 0.8057 (mt) REVERT: D 206 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7079 (mptt) REVERT: D 207 LYS cc_start: 0.8518 (mppt) cc_final: 0.8129 (mppt) REVERT: D 230 HIS cc_start: 0.7243 (t-90) cc_final: 0.6856 (t70) REVERT: D 234 ASP cc_start: 0.6857 (m-30) cc_final: 0.6603 (m-30) REVERT: D 257 LYS cc_start: 0.8172 (mttp) cc_final: 0.7735 (mttm) REVERT: D 266 GLU cc_start: 0.6000 (tt0) cc_final: 0.4383 (tt0) REVERT: D 353 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (p) REVERT: D 405 PHE cc_start: 0.8331 (m-80) cc_final: 0.7942 (m-80) REVERT: D 484 VAL cc_start: 0.8471 (t) cc_final: 0.8124 (m) REVERT: D 541 ASN cc_start: 0.7754 (t0) cc_final: 0.7495 (t0) REVERT: D 651 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7345 (tt) REVERT: D 706 SER cc_start: 0.8296 (t) cc_final: 0.7854 (p) REVERT: A 8 ILE cc_start: 0.7694 (mt) cc_final: 0.7116 (mp) REVERT: A 23 TRP cc_start: 0.5798 (t60) cc_final: 0.5411 (t-100) REVERT: A 62 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5464 (tp) REVERT: A 189 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7421 (mtmt) REVERT: A 198 ASP cc_start: 0.7244 (t0) cc_final: 0.6906 (t0) REVERT: A 355 TRP cc_start: 0.7625 (t-100) cc_final: 0.7108 (t-100) REVERT: A 415 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6976 (tm-30) REVERT: A 465 GLU cc_start: 0.7758 (tt0) cc_final: 0.7504 (tt0) REVERT: A 624 GLU cc_start: 0.7800 (mp0) cc_final: 0.7388 (mp0) REVERT: A 630 LYS cc_start: 0.8284 (mttm) cc_final: 0.8054 (mttp) REVERT: A 703 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8364 (ptpp) REVERT: A 866 ILE cc_start: 0.8436 (mt) cc_final: 0.8112 (mt) REVERT: A 1485 ASN cc_start: 0.7646 (t0) cc_final: 0.7398 (t0) REVERT: A 1487 TRP cc_start: 0.7611 (p-90) cc_final: 0.7366 (p-90) outliers start: 42 outliers final: 35 residues processed: 366 average time/residue: 0.1288 time to fit residues: 67.0496 Evaluate side-chains 378 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 chunk 145 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN A 276 GLN A 455 HIS A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.151464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139617 restraints weight = 21467.946| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.09 r_work: 0.3735 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15556 Z= 0.141 Angle : 0.630 12.630 21287 Z= 0.312 Chirality : 0.043 0.353 2406 Planarity : 0.004 0.054 2524 Dihedral : 15.247 179.989 2734 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.05 % Rotamer: Outliers : 2.75 % Allowed : 20.64 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1798 helix: 0.87 (0.21), residues: 623 sheet: -0.48 (0.34), residues: 240 loop : -1.30 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 120 TYR 0.019 0.001 TYR A 18 PHE 0.023 0.001 PHE D 254 TRP 0.044 0.001 TRP A1487 HIS 0.005 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00320 (15541) covalent geometry : angle 0.61165 (21272) hydrogen bonds : bond 0.03774 ( 539) hydrogen bonds : angle 4.61892 ( 1657) metal coordination : bond 0.00962 ( 15) metal coordination : angle 5.64223 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7424 (tm-30) REVERT: D 91 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7103 (mm-30) REVERT: D 148 LEU cc_start: 0.8311 (mt) cc_final: 0.8037 (mt) REVERT: D 206 LYS cc_start: 0.7398 (ptpp) cc_final: 0.7114 (mptt) REVERT: D 207 LYS cc_start: 0.8503 (mppt) cc_final: 0.8108 (mppt) REVERT: D 214 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7084 (mt-10) REVERT: D 216 MET cc_start: 0.6216 (tpp) cc_final: 0.5038 (ttp) REVERT: D 230 HIS cc_start: 0.7211 (t-90) cc_final: 0.6810 (t70) REVERT: D 234 ASP cc_start: 0.6893 (m-30) cc_final: 0.6644 (m-30) REVERT: D 252 ARG cc_start: 0.7089 (mpt-90) cc_final: 0.6777 (mtt90) REVERT: D 266 GLU cc_start: 0.5834 (tt0) cc_final: 0.4180 (tt0) REVERT: D 353 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8057 (p) REVERT: D 405 PHE cc_start: 0.8320 (m-80) cc_final: 0.7894 (m-80) REVERT: D 477 PHE cc_start: 0.7608 (t80) cc_final: 0.7296 (t80) REVERT: D 484 VAL cc_start: 0.8465 (t) cc_final: 0.8119 (m) REVERT: D 541 ASN cc_start: 0.7718 (t0) cc_final: 0.7468 (t0) REVERT: D 651 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7243 (tt) REVERT: D 706 SER cc_start: 0.8284 (t) cc_final: 0.7831 (p) REVERT: A 23 TRP cc_start: 0.5745 (t60) cc_final: 0.5377 (t-100) REVERT: A 62 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5334 (tp) REVERT: A 189 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7430 (mtmt) REVERT: A 198 ASP cc_start: 0.7247 (t0) cc_final: 0.6900 (t0) REVERT: A 355 TRP cc_start: 0.7612 (t-100) cc_final: 0.7109 (t-100) REVERT: A 415 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 465 GLU cc_start: 0.7720 (tt0) cc_final: 0.7459 (tt0) REVERT: A 624 GLU cc_start: 0.7776 (mp0) cc_final: 0.7326 (mp0) REVERT: A 630 LYS cc_start: 0.8226 (mttm) cc_final: 0.7893 (mttp) REVERT: A 703 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8360 (ptpp) REVERT: A 866 ILE cc_start: 0.8416 (mt) cc_final: 0.8079 (mt) REVERT: A 1485 ASN cc_start: 0.7642 (t0) cc_final: 0.7379 (t0) REVERT: A 1487 TRP cc_start: 0.7453 (p-90) cc_final: 0.7092 (p-90) outliers start: 38 outliers final: 32 residues processed: 364 average time/residue: 0.1318 time to fit residues: 68.1927 Evaluate side-chains 373 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 338 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 115 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 ASN A 276 GLN A 776 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138056 restraints weight = 21720.242| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.20 r_work: 0.3710 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15556 Z= 0.172 Angle : 0.656 12.795 21287 Z= 0.323 Chirality : 0.044 0.398 2406 Planarity : 0.004 0.052 2524 Dihedral : 15.275 179.297 2734 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.11 % Allowed : 20.42 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1798 helix: 0.82 (0.20), residues: 621 sheet: -0.53 (0.34), residues: 240 loop : -1.30 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 120 TYR 0.021 0.002 TYR A 18 PHE 0.020 0.002 PHE A1433 TRP 0.038 0.002 TRP A1487 HIS 0.004 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00392 (15541) covalent geometry : angle 0.63688 (21272) hydrogen bonds : bond 0.03904 ( 539) hydrogen bonds : angle 4.65567 ( 1657) metal coordination : bond 0.01034 ( 15) metal coordination : angle 5.90074 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7504 (tt0) REVERT: D 148 LEU cc_start: 0.8262 (mt) cc_final: 0.8000 (mt) REVERT: D 206 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7133 (mptt) REVERT: D 207 LYS cc_start: 0.8510 (mppt) cc_final: 0.8127 (mppt) REVERT: D 216 MET cc_start: 0.6076 (tpp) cc_final: 0.5424 (ttp) REVERT: D 230 HIS cc_start: 0.7275 (t-90) cc_final: 0.6882 (t70) REVERT: D 234 ASP cc_start: 0.6964 (m-30) cc_final: 0.6712 (m-30) REVERT: D 266 GLU cc_start: 0.6029 (tt0) cc_final: 0.4024 (tt0) REVERT: D 353 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8079 (p) REVERT: D 405 PHE cc_start: 0.8345 (m-80) cc_final: 0.7954 (m-80) REVERT: D 484 VAL cc_start: 0.8454 (t) cc_final: 0.8126 (m) REVERT: D 541 ASN cc_start: 0.7777 (t0) cc_final: 0.7520 (t0) REVERT: D 651 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7223 (tt) REVERT: D 706 SER cc_start: 0.8351 (t) cc_final: 0.7926 (p) REVERT: A 8 ILE cc_start: 0.7631 (mt) cc_final: 0.7124 (mp) REVERT: A 23 TRP cc_start: 0.5799 (t60) cc_final: 0.5433 (t-100) REVERT: A 62 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5422 (tp) REVERT: A 189 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7448 (mtmt) REVERT: A 198 ASP cc_start: 0.7273 (t0) cc_final: 0.6921 (t0) REVERT: A 351 LYS cc_start: 0.7841 (mptt) cc_final: 0.7532 (mmtt) REVERT: A 355 TRP cc_start: 0.7627 (t-100) cc_final: 0.7128 (t-100) REVERT: A 415 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7001 (tm-30) REVERT: A 465 GLU cc_start: 0.7748 (tt0) cc_final: 0.7481 (tt0) REVERT: A 624 GLU cc_start: 0.7809 (mp0) cc_final: 0.7342 (mp0) REVERT: A 866 ILE cc_start: 0.8441 (mt) cc_final: 0.8108 (mt) REVERT: A 1485 ASN cc_start: 0.7657 (t0) cc_final: 0.7428 (t0) REVERT: A 1487 TRP cc_start: 0.7376 (p-90) cc_final: 0.7130 (p-90) REVERT: A 1561 LYS cc_start: 0.8110 (tptm) cc_final: 0.7901 (tptm) outliers start: 43 outliers final: 32 residues processed: 361 average time/residue: 0.1388 time to fit residues: 71.9835 Evaluate side-chains 373 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1414 CYS Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain A residue 1560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 112 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 41 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 GLN A 276 GLN A 776 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140107 restraints weight = 21436.273| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.09 r_work: 0.3740 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15556 Z= 0.138 Angle : 0.635 12.619 21287 Z= 0.313 Chirality : 0.043 0.385 2406 Planarity : 0.004 0.054 2524 Dihedral : 15.249 179.831 2734 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 2.61 % Allowed : 21.07 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1798 helix: 0.87 (0.21), residues: 620 sheet: -0.49 (0.34), residues: 239 loop : -1.29 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 120 TYR 0.020 0.001 TYR A 429 PHE 0.020 0.001 PHE D 254 TRP 0.032 0.002 TRP A 82 HIS 0.005 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00316 (15541) covalent geometry : angle 0.61755 (21272) hydrogen bonds : bond 0.03721 ( 539) hydrogen bonds : angle 4.57407 ( 1657) metal coordination : bond 0.00786 ( 15) metal coordination : angle 5.53184 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.81 seconds wall clock time: 63 minutes 19.45 seconds (3799.45 seconds total)