Starting phenix.real_space_refine on Sat Feb 17 01:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8y_33686/02_2024/7y8y_33686.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 55 5.49 5 S 59 5.16 5 C 10611 2.51 5 N 2951 2.21 5 O 3343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 18": "OD1" <-> "OD2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 875": "OD1" <-> "OD2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 938": "OD1" <-> "OD2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A ASP 1424": "OD1" <-> "OD2" Residue "A TYR 1436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17023 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5468 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1291, 10378 Classifications: {'peptide': 1291} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 62, 'TRANS': 1227} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 780 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 21, 'rna3p': 15} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 393 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 4} Link IDs: {'rna3p': 17} 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 9104 SG CYS A 491 47.965 49.179 114.332 1.00 41.16 S ATOM 9172 SG CYS A 501 47.679 48.247 117.979 1.00 36.50 S ATOM 9186 SG CYS A 503 44.704 47.764 115.662 1.00 32.57 S ATOM 9208 SG CYS A 506 47.602 45.453 115.318 1.00 33.14 S ATOM 13309 SG CYS A1018 59.236 69.245 52.513 1.00 67.92 S ATOM 13536 SG CYS A1406 60.052 70.341 56.116 1.00 58.40 S ATOM 13587 SG CYS A1414 57.111 71.800 54.150 1.00 55.83 S ATOM 13604 SG CYS A1417 56.898 68.283 55.418 1.00 43.89 S ATOM 6144 SG CYS A 88 52.917 25.609 139.837 1.00 40.36 S ATOM 6415 SG CYS A 121 54.618 22.965 142.014 1.00 68.04 S ATOM 6461 SG CYS A 127 53.378 22.155 138.467 1.00 36.89 S ATOM 6485 SG CYS A 130 56.407 24.331 138.934 1.00 43.43 S ATOM 11179 SG CYS A 750 51.016 68.821 89.708 1.00 67.10 S ATOM 11192 SG CYS A 752 47.968 67.670 87.742 1.00 50.21 S ATOM 11214 SG CYS A 755 50.020 65.099 89.750 1.00 50.68 S Time building chain proxies: 8.98, per 1000 atoms: 0.53 Number of scatterers: 17023 At special positions: 0 Unit cell: (107.8, 106.7, 167.2, 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 59 16.00 P 55 15.00 O 3343 8.00 N 2951 7.00 C 10611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1406 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 121 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 755 " Number of angles added : 21 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 37.6% alpha, 16.7% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'B' and resid 14 through 30 removed outlier: 3.747A pdb=" N ILE B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.160A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.566A pdb=" N ILE B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.945A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 163 through 177 removed outlier: 4.085A pdb=" N ILE B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.535A pdb=" N LYS B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.698A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.501A pdb=" N LYS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.918A pdb=" N LEU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.743A pdb=" N HIS B 493 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 494 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.845A pdb=" N SER B 500 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.693A pdb=" N ILE B 573 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 607 through 614 removed outlier: 3.738A pdb=" N VAL B 614 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 653 removed outlier: 4.053A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.879A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.850A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.068A pdb=" N LYS A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 31 " --> pdb=" O ALA A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 31' Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.748A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 267 through 287 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.806A pdb=" N THR A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.538A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.588A pdb=" N ILE A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.748A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 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 630 through 636 removed outlier: 3.771A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.617A pdb=" N ALA A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 712 Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.536A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.576A pdb=" N GLU A 779 " --> pdb=" O ASN A 776 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 780' Processing helix chain 'A' and resid 831 through 848 removed outlier: 3.518A pdb=" N GLY A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.523A pdb=" N VAL A 858 " --> pdb=" O LYS A 855 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 855 through 859' Processing helix chain 'A' and resid 873 through 884 Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.984A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 4.257A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.721A pdb=" N LEU A1532 " --> pdb=" O ARG A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.783A pdb=" N ILE A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1603 " --> pdb=" O ILE A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1628 removed outlier: 3.655A pdb=" N LEU A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1668 removed outlier: 3.650A pdb=" N GLY A1667 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A1668 " --> pdb=" O LYS A1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1664 through 1668' Processing helix chain 'A' and resid 1673 through 1682 Processing sheet with id=AA1, first strand: chain 'B' and resid 425 through 431 removed outlier: 3.586A pdb=" N SER B 425 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 416 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 431 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 406 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 402 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 540 removed outlier: 7.105A pdb=" N VAL B 537 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LEU B 583 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 539 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 580 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 659 " --> pdb=" O ARG B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.842A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 597 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.326A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.783A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 53 through 58 current: chain 'A' and resid 233 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.214A 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 173 through 181 removed outlier: 4.621A pdb=" N ARG A 180 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.701A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 415 " --> pdb=" O TRP A 612 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 589 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.701A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 415 " --> pdb=" O TRP A 612 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 647 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.528A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 533 removed outlier: 3.691A pdb=" N ALA A 532 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.513A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.513A pdb=" N ARG A 719 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 674 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 708 removed outlier: 3.620A pdb=" N ALA A 713 " --> pdb=" O ASN A 708 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 925 through 927 Processing sheet with id=AB9, first strand: chain 'A' and resid 997 through 998 removed outlier: 7.198A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 952 " --> pdb=" O PHE A1524 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.608A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY A 952 " --> pdb=" O PHE A1524 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1453 through 1455 591 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4410 1.33 - 1.45: 3495 1.45 - 1.57: 9422 1.57 - 1.69: 108 1.69 - 1.81: 83 Bond restraints: 17518 Sorted by residual: bond pdb=" C LYS A1553 " pdb=" N PRO A1554 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.06e+00 bond pdb=" CB GLU B 23 " pdb=" CG GLU B 23 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C ASN A1449 " pdb=" N PRO A1450 " ideal model delta sigma weight residual 1.332 1.349 -0.018 1.30e-02 5.92e+03 1.89e+00 bond pdb=" CB GLU A 639 " pdb=" CG GLU A 639 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB ARG B 16 " pdb=" CG ARG B 16 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 17513 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 781 107.06 - 113.82: 9640 113.82 - 120.57: 6820 120.57 - 127.33: 6352 127.33 - 134.08: 309 Bond angle restraints: 23902 Sorted by residual: angle pdb=" C ASP B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" CA LYS A 147 " pdb=" CB LYS A 147 " pdb=" CG LYS A 147 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" C LEU A1495 " pdb=" N GLU A1496 " pdb=" CA GLU A1496 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CB LYS B 389 " pdb=" CG LYS B 389 " pdb=" CD LYS B 389 " ideal model delta sigma weight residual 111.30 120.08 -8.78 2.30e+00 1.89e-01 1.46e+01 angle pdb=" N LYS B 85 " pdb=" CA LYS B 85 " pdb=" C LYS B 85 " ideal model delta sigma weight residual 112.58 108.25 4.33 1.22e+00 6.72e-01 1.26e+01 ... (remaining 23897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 10117 35.34 - 70.68: 435 70.68 - 106.01: 35 106.01 - 141.35: 2 141.35 - 176.69: 9 Dihedral angle restraints: 10598 sinusoidal: 4914 harmonic: 5684 Sorted by residual: dihedral pdb=" O4' U E -4 " pdb=" C1' U E -4 " pdb=" N1 U E -4 " pdb=" C2 U E -4 " ideal model delta sinusoidal sigma weight residual 200.00 33.31 166.69 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U D 7 " pdb=" C1' U D 7 " pdb=" N1 U D 7 " pdb=" C2 U D 7 " ideal model delta sinusoidal sigma weight residual 200.00 33.47 166.53 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C D 1 " pdb=" C1' C D 1 " pdb=" N1 C D 1 " pdb=" C2 C D 1 " ideal model delta sinusoidal sigma weight residual -160.00 5.18 -165.18 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 10595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1924 0.040 - 0.079: 496 0.079 - 0.119: 153 0.119 - 0.159: 25 0.159 - 0.198: 5 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1' U D 7 " pdb=" O4' U D 7 " pdb=" C2' U D 7 " pdb=" N1 U D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU A 691 " pdb=" CB LEU A 691 " pdb=" CD1 LEU A 691 " pdb=" CD2 LEU A 691 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ASP A 190 " pdb=" N ASP A 190 " pdb=" C ASP A 190 " pdb=" CB ASP A 190 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2600 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1463 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO A1464 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A1464 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1464 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C D 9 " -0.028 2.00e-02 2.50e+03 1.48e-02 4.93e+00 pdb=" N1 C D 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C D 9 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C D 9 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C D 9 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C D 9 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C D 9 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C D 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 146 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ASN A 146 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN A 146 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 147 " 0.012 2.00e-02 2.50e+03 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1421 2.74 - 3.28: 15445 3.28 - 3.82: 26245 3.82 - 4.36: 31196 4.36 - 4.90: 54802 Nonbonded interactions: 129109 Sorted by model distance: nonbonded pdb=" O THR A 456 " pdb=" OG1 THR A 456 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR A 739 " pdb=" OD1 ASP A 741 " model vdw 2.215 2.440 nonbonded pdb=" N GLU B 181 " pdb=" OE1 GLU B 181 " model vdw 2.226 2.520 nonbonded pdb=" O LEU A 961 " pdb=" NZ LYS A1514 " model vdw 2.262 2.520 nonbonded pdb=" OG SER A 680 " pdb=" O GLY A 859 " model vdw 2.272 2.440 ... (remaining 129104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.300 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 53.000 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 0.042 17518 Z= 0.165 Angle : 0.607 11.452 23902 Z= 0.327 Chirality : 0.040 0.198 2603 Planarity : 0.004 0.065 2878 Dihedral : 18.861 176.689 6944 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 2.51 % Allowed : 24.13 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1957 helix: 1.67 (0.22), residues: 626 sheet: -0.07 (0.32), residues: 268 loop : -1.83 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 26 HIS 0.003 0.001 HIS A1617 PHE 0.029 0.001 PHE A 795 TYR 0.020 0.001 TYR B 76 ARG 0.008 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 2.016 Fit side-chains REVERT: A 880 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5829 (mp) outliers start: 43 outliers final: 38 residues processed: 166 average time/residue: 1.0856 time to fit residues: 206.3089 Evaluate side-chains 160 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 394 HIS ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17518 Z= 0.286 Angle : 0.629 10.227 23902 Z= 0.325 Chirality : 0.043 0.218 2603 Planarity : 0.004 0.054 2878 Dihedral : 17.641 177.126 3038 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.51 % Favored : 92.34 % Rotamer: Outliers : 5.89 % Allowed : 20.45 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1957 helix: 1.29 (0.21), residues: 636 sheet: -0.18 (0.32), residues: 270 loop : -1.92 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 26 HIS 0.006 0.001 HIS B 493 PHE 0.018 0.002 PHE B 491 TYR 0.021 0.002 TYR B 704 ARG 0.007 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 134 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: B 395 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: B 631 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5839 (mt) REVERT: A 415 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: A 697 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7017 (mmt90) REVERT: A 745 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 846 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6722 (ttt180) outliers start: 101 outliers final: 51 residues processed: 213 average time/residue: 1.1441 time to fit residues: 276.5714 Evaluate side-chains 183 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 126 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 GLN A 116 ASN A 498 GLN A 668 GLN ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17518 Z= 0.251 Angle : 0.611 10.044 23902 Z= 0.315 Chirality : 0.043 0.225 2603 Planarity : 0.004 0.048 2878 Dihedral : 17.432 177.640 3013 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.15 % Rotamer: Outliers : 5.65 % Allowed : 21.50 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1957 helix: 1.26 (0.21), residues: 637 sheet: -0.26 (0.32), residues: 270 loop : -1.97 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 278 HIS 0.004 0.001 HIS B 493 PHE 0.016 0.002 PHE B 491 TYR 0.020 0.001 TYR B 704 ARG 0.007 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 129 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7408 (tptm) REVERT: B 395 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: B 508 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7717 (mmtt) REVERT: B 559 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5547 (mp10) REVERT: B 631 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5822 (mt) REVERT: B 663 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8045 (tttm) REVERT: A 229 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: A 293 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4674 (tp) REVERT: A 415 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: A 745 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 846 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6729 (ttt180) REVERT: A 880 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5871 (mp) outliers start: 97 outliers final: 61 residues processed: 206 average time/residue: 1.1593 time to fit residues: 271.5077 Evaluate side-chains 195 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 122 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Chi-restraints excluded: chain A residue 1671 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17518 Z= 0.283 Angle : 0.637 9.223 23902 Z= 0.329 Chirality : 0.044 0.237 2603 Planarity : 0.005 0.048 2878 Dihedral : 17.487 176.508 3013 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.51 % Favored : 92.28 % Rotamer: Outliers : 6.29 % Allowed : 22.14 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1957 helix: 1.17 (0.21), residues: 637 sheet: -0.37 (0.32), residues: 267 loop : -2.01 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 PHE 0.020 0.002 PHE B 491 TYR 0.021 0.002 TYR B 704 ARG 0.008 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 126 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: B 22 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7386 (tptm) REVERT: B 64 THR cc_start: 0.5421 (OUTLIER) cc_final: 0.5108 (t) REVERT: B 395 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 508 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: B 663 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8054 (tttm) REVERT: A 293 ILE cc_start: 0.5102 (OUTLIER) cc_final: 0.4721 (tp) REVERT: A 415 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: A 697 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6949 (mmt90) REVERT: A 745 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: A 846 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6758 (ttt180) REVERT: A 880 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5924 (mp) REVERT: A 959 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7509 (tt0) outliers start: 108 outliers final: 65 residues processed: 211 average time/residue: 1.2060 time to fit residues: 288.0134 Evaluate side-chains 195 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 118 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.0020 chunk 110 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 498 GLN ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17518 Z= 0.147 Angle : 0.549 8.698 23902 Z= 0.281 Chirality : 0.040 0.221 2603 Planarity : 0.004 0.046 2878 Dihedral : 17.248 177.965 3012 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.43 % Rotamer: Outliers : 4.66 % Allowed : 24.18 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1957 helix: 1.55 (0.21), residues: 638 sheet: -0.30 (0.32), residues: 274 loop : -1.85 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 330 HIS 0.005 0.001 HIS B 699 PHE 0.020 0.001 PHE A 795 TYR 0.014 0.001 TYR B 704 ARG 0.010 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 125 time to evaluate : 1.857 Fit side-chains REVERT: B 210 HIS cc_start: 0.6429 (m90) cc_final: 0.6217 (m90) REVERT: B 348 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6162 (t80) REVERT: B 631 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5752 (mt) REVERT: B 663 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.8029 (tttm) REVERT: A 293 ILE cc_start: 0.4947 (OUTLIER) cc_final: 0.4562 (tp) REVERT: A 415 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6870 (tp30) REVERT: A 697 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6905 (mmt90) REVERT: A 745 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 846 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6646 (ttt180) REVERT: A 1588 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6519 (mmt180) outliers start: 80 outliers final: 39 residues processed: 187 average time/residue: 1.2436 time to fit residues: 262.5056 Evaluate side-chains 164 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 116 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 161 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN ** A1576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17518 Z= 0.364 Angle : 0.695 9.455 23902 Z= 0.358 Chirality : 0.046 0.241 2603 Planarity : 0.005 0.053 2878 Dihedral : 17.430 177.965 3004 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.23 % Favored : 91.57 % Rotamer: Outliers : 5.71 % Allowed : 23.54 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1957 helix: 1.12 (0.21), residues: 636 sheet: -0.31 (0.33), residues: 258 loop : -2.06 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 612 HIS 0.006 0.001 HIS B 493 PHE 0.022 0.002 PHE B 491 TYR 0.022 0.002 TYR B 704 ARG 0.007 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 122 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: B 64 THR cc_start: 0.5404 (OUTLIER) cc_final: 0.5112 (t) REVERT: B 395 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: B 508 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7790 (mmtt) REVERT: B 631 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6101 (mt) REVERT: B 663 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8067 (tttm) REVERT: A 55 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7578 (mtpt) REVERT: A 212 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6983 (ttm110) REVERT: A 293 ILE cc_start: 0.5105 (OUTLIER) cc_final: 0.4720 (tp) REVERT: A 415 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: A 697 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6942 (mmt90) REVERT: A 745 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 846 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6846 (ttt180) REVERT: A 880 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.5883 (mp) REVERT: A 1588 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6631 (mmt180) REVERT: A 1598 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8580 (tt) REVERT: A 1677 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7737 (ttp-170) outliers start: 98 outliers final: 53 residues processed: 197 average time/residue: 1.1932 time to fit residues: 265.9404 Evaluate side-chains 186 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 118 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 627 CYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 193 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 119 optimal weight: 0.0040 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17518 Z= 0.151 Angle : 0.562 9.417 23902 Z= 0.289 Chirality : 0.041 0.227 2603 Planarity : 0.004 0.048 2878 Dihedral : 17.190 174.460 3003 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % Rotamer: Outliers : 3.79 % Allowed : 25.87 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1957 helix: 1.56 (0.21), residues: 637 sheet: -0.24 (0.32), residues: 273 loop : -1.89 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.005 0.001 HIS B 699 PHE 0.022 0.001 PHE A 795 TYR 0.014 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 123 time to evaluate : 2.039 Fit side-chains REVERT: B 64 THR cc_start: 0.5313 (OUTLIER) cc_final: 0.4982 (t) REVERT: B 348 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6203 (t80) REVERT: B 631 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5779 (mt) REVERT: B 663 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: A 6 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6464 (mmm) REVERT: A 212 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6903 (ttm110) REVERT: A 293 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4732 (tp) REVERT: A 415 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: A 697 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6876 (mmt90) REVERT: A 745 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 846 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6663 (ttt180) REVERT: A 1588 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6514 (mmt180) REVERT: A 1677 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7720 (ttp-170) outliers start: 65 outliers final: 41 residues processed: 172 average time/residue: 1.2621 time to fit residues: 244.9208 Evaluate side-chains 172 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 119 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN A 434 GLN A 498 GLN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17518 Z= 0.159 Angle : 0.557 10.127 23902 Z= 0.286 Chirality : 0.041 0.219 2603 Planarity : 0.004 0.051 2878 Dihedral : 17.142 175.017 3001 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.44 % Favored : 93.41 % Rotamer: Outliers : 3.96 % Allowed : 25.70 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1957 helix: 1.66 (0.21), residues: 636 sheet: -0.19 (0.32), residues: 273 loop : -1.84 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.003 0.001 HIS A1617 PHE 0.024 0.001 PHE A 795 TYR 0.015 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 121 time to evaluate : 1.823 Fit side-chains REVERT: B 219 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7779 (p) REVERT: B 348 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6189 (t80) REVERT: B 663 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8064 (tttm) REVERT: A 212 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6825 (ttm110) REVERT: A 293 ILE cc_start: 0.5051 (OUTLIER) cc_final: 0.4663 (tp) REVERT: A 415 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: A 697 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6709 (tpp-160) REVERT: A 745 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 1588 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6505 (mmt180) REVERT: A 1677 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7699 (ttp-170) outliers start: 68 outliers final: 44 residues processed: 172 average time/residue: 1.2352 time to fit residues: 240.7340 Evaluate side-chains 174 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 121 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 348 PHE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1588 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 chunk 163 optimal weight: 0.0020 chunk 170 optimal weight: 0.0980 chunk 179 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17518 Z= 0.137 Angle : 0.541 9.581 23902 Z= 0.277 Chirality : 0.040 0.212 2603 Planarity : 0.004 0.051 2878 Dihedral : 17.065 176.358 2998 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.62 % Favored : 94.23 % Rotamer: Outliers : 2.97 % Allowed : 26.63 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1957 helix: 1.77 (0.21), residues: 638 sheet: -0.11 (0.32), residues: 273 loop : -1.75 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.005 0.001 HIS B 699 PHE 0.025 0.001 PHE A 795 TYR 0.012 0.001 TYR B 704 ARG 0.015 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 125 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: B 663 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8059 (tttm) REVERT: A 212 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6716 (ttm110) REVERT: A 293 ILE cc_start: 0.5062 (OUTLIER) cc_final: 0.4684 (tp) REVERT: A 415 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: A 697 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6818 (mmt90) REVERT: A 745 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: A 1677 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7686 (ttp-170) outliers start: 51 outliers final: 38 residues processed: 164 average time/residue: 1.3324 time to fit residues: 246.1283 Evaluate side-chains 165 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 90 optimal weight: 0.0570 chunk 132 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17518 Z= 0.157 Angle : 0.550 9.222 23902 Z= 0.281 Chirality : 0.040 0.209 2603 Planarity : 0.004 0.052 2878 Dihedral : 17.043 177.203 2993 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 27.04 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1957 helix: 1.78 (0.21), residues: 637 sheet: -0.08 (0.32), residues: 273 loop : -1.77 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 278 HIS 0.004 0.001 HIS B 699 PHE 0.027 0.001 PHE A 795 TYR 0.015 0.001 TYR B 704 ARG 0.012 0.000 ARG A 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3914 Ramachandran restraints generated. 1957 Oldfield, 0 Emsley, 1957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: B 663 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: A 212 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6778 (ttm110) REVERT: A 293 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4693 (tp) REVERT: A 415 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: A 697 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6683 (tpp-160) REVERT: A 745 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 1475 ILE cc_start: 0.7681 (pt) cc_final: 0.7463 (pt) REVERT: A 1677 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7633 (ttp-170) outliers start: 45 outliers final: 38 residues processed: 156 average time/residue: 1.2853 time to fit residues: 225.8557 Evaluate side-chains 166 residues out of total 1733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 1411 ASP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1652 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.0770 chunk 48 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 146 ASN A 498 GLN ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137470 restraints weight = 22426.332| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.78 r_work: 0.3466 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17518 Z= 0.158 Angle : 0.554 9.113 23902 Z= 0.283 Chirality : 0.040 0.206 2603 Planarity : 0.004 0.052 2878 Dihedral : 17.014 177.581 2991 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 3.21 % Allowed : 26.52 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1957 helix: 1.82 (0.21), residues: 636 sheet: -0.05 (0.32), residues: 273 loop : -1.76 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 278 HIS 0.004 0.001 HIS B 699 PHE 0.026 0.001 PHE A 795 TYR 0.015 0.001 TYR B 704 ARG 0.009 0.000 ARG A 719 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5085.08 seconds wall clock time: 91 minutes 46.11 seconds (5506.11 seconds total)