Starting phenix.real_space_refine on Sun Dec 10 22:53:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7o_31001/12_2023/7e7o_31001_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 86 5.16 5 C 10225 2.51 5 N 2609 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 948": "NH1" <-> "NH2" Residue "A TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A ASP 999": "OD1" <-> "OD2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A TYR 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1108": "NH1" <-> "NH2" Residue "A ASP 1121": "OD1" <-> "OD2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1204": "OD1" <-> "OD2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1362": "NH1" <-> "NH2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A GLU 1452": "OE1" <-> "OE2" Residue "A TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1493": "NH1" <-> "NH2" Residue "A ARG 1517": "NH1" <-> "NH2" Residue "A ARG 1528": "NH1" <-> "NH2" Residue "A PHE 1550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1585": "NH1" <-> "NH2" Residue "A ARG 1596": "NH1" <-> "NH2" Residue "A GLU 1597": "OE1" <-> "OE2" Residue "A GLU 1601": "OE1" <-> "OE2" Residue "A PHE 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1647": "NH1" <-> "NH2" Residue "A GLU 1666": "OE1" <-> "OE2" Residue "A TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A ASP 1731": "OD1" <-> "OD2" Residue "A TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1824": "NH1" <-> "NH2" Residue "A PHE 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1860": "NH1" <-> "NH2" Residue "A ARG 1898": "NH1" <-> "NH2" Residue "A GLU 1923": "OE1" <-> "OE2" Residue "A ARG 1925": "NH1" <-> "NH2" Residue "A ARG 1939": "NH1" <-> "NH2" Residue "A GLU 1942": "OE1" <-> "OE2" Residue "A ARG 1957": "NH1" <-> "NH2" Residue "A PHE 2020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2021": "OD1" <-> "OD2" Residue "A ASP 2024": "OD1" <-> "OD2" Residue "A ARG 2030": "NH1" <-> "NH2" Residue "A ARG 2038": "NH1" <-> "NH2" Residue "A ARG 2040": "NH1" <-> "NH2" Residue "A GLU 2048": "OE1" <-> "OE2" Residue "A ARG 2077": "NH1" <-> "NH2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "A ARG 2118": "NH1" <-> "NH2" Residue "A GLU 2119": "OE1" <-> "OE2" Residue "A ARG 2121": "NH1" <-> "NH2" Residue "A GLU 2131": "OE1" <-> "OE2" Residue "A GLU 2134": "OE1" <-> "OE2" Residue "A ARG 2139": "NH1" <-> "NH2" Residue "A ARG 2149": "NH1" <-> "NH2" Residue "A PHE 2161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2201": "NH1" <-> "NH2" Residue "A TYR 2203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2233": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2003, 15372 Classifications: {'peptide': 2003} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 98, 'TRANS': 1904} Chain breaks: 12 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 789 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 376 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 322 Unusual residues: {'3PE': 3, 'HZL': 1, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.80, per 1000 atoms: 0.56 Number of scatterers: 15816 At special positions: 0 Unit cell: (101.52, 101.52, 239.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 4 15.00 O 2892 8.00 N 2609 7.00 C 10225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=1.84 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=1.37 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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=1, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " " BMA N 3 " - " BMA N 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " BETA1-6 " BMA E 3 " - " BMA E 5 " " BMA N 3 " - " BMA N 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 444 " " NAG A2303 " - " ASN A 504 " " NAG A2304 " - " ASN A1457 " " NAG A2305 " - " ASN A1469 " " NAG A2306 " - " ASN A1588 " " NAG A2307 " - " ASN A1662 " " NAG E 1 " - " ASN A 415 " " NAG N 1 " - " ASN A1529 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 2.8 seconds 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 8 sheets defined 44.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.770A pdb=" N GLN A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 removed outlier: 4.106A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.228A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.795A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 4.382A pdb=" N GLN A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 234 through 237 No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 274 through 288 removed outlier: 4.908A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.831A pdb=" N GLN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.597A pdb=" N ALA A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 441 removed outlier: 3.906A pdb=" N ASN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 3.513A pdb=" N PHE A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 451 No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.632A pdb=" N ARG A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 3.975A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 608 through 621 Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.794A pdb=" N ASN A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 666 through 679 removed outlier: 3.808A pdb=" N SER A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.826A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 721 removed outlier: 3.700A pdb=" N LEU A 702 " --> pdb=" O CYS A 698 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 753 removed outlier: 3.748A pdb=" N ALA A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 776 removed outlier: 4.674A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 788 through 791 No H-bonds generated for 'chain 'A' and resid 788 through 791' Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 798 through 814 removed outlier: 3.640A pdb=" N GLY A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 removed outlier: 3.786A pdb=" N MET A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 976 Processing helix chain 'A' and resid 1020 through 1032 removed outlier: 3.520A pdb=" N GLY A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1048 removed outlier: 3.958A pdb=" N GLU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.668A pdb=" N ALA A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1105 Processing helix chain 'A' and resid 1122 through 1125 No H-bonds generated for 'chain 'A' and resid 1122 through 1125' Processing helix chain 'A' and resid 1144 through 1151 removed outlier: 3.596A pdb=" N PHE A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1213 removed outlier: 4.254A pdb=" N ASP A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1252 removed outlier: 3.809A pdb=" N PHE A1247 " --> pdb=" O TYR A1243 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1249 " --> pdb=" O SER A1245 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A1251 " --> pdb=" O PHE A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 removed outlier: 3.543A pdb=" N PHE A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A1277 " --> pdb=" O PHE A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 removed outlier: 3.823A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A1365 " --> pdb=" O LYS A1361 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A1366 " --> pdb=" O ARG A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1374 No H-bonds generated for 'chain 'A' and resid 1371 through 1374' Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 3.539A pdb=" N ALA A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1409 No H-bonds generated for 'chain 'A' and resid 1407 through 1409' Processing helix chain 'A' and resid 1468 through 1474 Processing helix chain 'A' and resid 1530 through 1536 removed outlier: 4.457A pdb=" N VAL A1535 " --> pdb=" O SER A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1545 removed outlier: 4.301A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1586 removed outlier: 3.785A pdb=" N PHE A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1598 removed outlier: 3.611A pdb=" N GLU A1597 " --> pdb=" O PRO A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1605 No H-bonds generated for 'chain 'A' and resid 1602 through 1605' Processing helix chain 'A' and resid 1626 through 1640 removed outlier: 3.796A pdb=" N PHE A1630 " --> pdb=" O ALA A1626 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A1640 " --> pdb=" O ASN A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 Processing helix chain 'A' and resid 1679 through 1689 removed outlier: 4.096A pdb=" N ILE A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1716 removed outlier: 3.595A pdb=" N ALA A1695 " --> pdb=" O SER A1691 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A1697 " --> pdb=" O VAL A1693 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A1698 " --> pdb=" O PRO A1694 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1699 " --> pdb=" O ALA A1695 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A1700 " --> pdb=" O SER A1696 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS A1708 " --> pdb=" O GLU A1704 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A1709 " --> pdb=" O ARG A1705 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS A1710 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N HIS A1711 " --> pdb=" O ASN A1707 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1712 " --> pdb=" O LYS A1708 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A1713 " --> pdb=" O SER A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1749 removed outlier: 3.757A pdb=" N MET A1733 " --> pdb=" O LEU A1729 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1782 removed outlier: 3.515A pdb=" N LEU A1766 " --> pdb=" O ALA A1762 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1769 " --> pdb=" O ALA A1765 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A1770 " --> pdb=" O LEU A1766 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) Proline residue: A1776 - end of helix removed outlier: 3.628A pdb=" N TYR A1779 " --> pdb=" O ILE A1775 " (cutoff:3.500A) Proline residue: A1780 - end of helix Processing helix chain 'A' and resid 1788 through 1805 removed outlier: 3.571A pdb=" N ALA A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A1800 " --> pdb=" O SER A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1809 through 1812 No H-bonds generated for 'chain 'A' and resid 1809 through 1812' Processing helix chain 'A' and resid 1822 through 1835 removed outlier: 3.882A pdb=" N ALA A1827 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1829 " --> pdb=" O PHE A1825 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A1834 " --> pdb=" O ARG A1830 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A1835 " --> pdb=" O LYS A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1857 removed outlier: 3.641A pdb=" N LEU A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A1849 " --> pdb=" O LEU A1845 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1885 removed outlier: 3.518A pdb=" N PHE A1880 " --> pdb=" O GLY A1876 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1889 through 1898 Processing helix chain 'A' and resid 1918 through 1926 Processing helix chain 'A' and resid 1979 through 1986 Processing helix chain 'A' and resid 2010 through 2013 Processing helix chain 'A' and resid 2029 through 2039 removed outlier: 3.850A pdb=" N TYR A2036 " --> pdb=" O HIS A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2058 removed outlier: 3.771A pdb=" N ILE A2047 " --> pdb=" O ALA A2044 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU A2048 " --> pdb=" O GLU A2045 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A2051 " --> pdb=" O GLU A2048 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A2058 " --> pdb=" O ILE A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2084 Processing helix chain 'A' and resid 2103 through 2117 removed outlier: 3.801A pdb=" N VAL A2112 " --> pdb=" O MET A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2154 through 2160 Processing helix chain 'A' and resid 2182 through 2191 removed outlier: 3.783A pdb=" N PHE A2188 " --> pdb=" O PRO A2184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A2189 " --> pdb=" O VAL A2185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A2191 " --> pdb=" O GLN A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2216 through 2219 No H-bonds generated for 'chain 'A' and resid 2216 through 2219' Processing helix chain 'A' and resid 2241 through 2250 Processing sheet with id= A, first strand: chain 'A' and resid 48 through 51 Processing sheet with id= B, first strand: chain 'A' and resid 550 through 552 Processing sheet with id= C, first strand: chain 'A' and resid 631 through 636 removed outlier: 8.681A pdb=" N TYR A1414 " --> pdb=" O TYR A1557 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY A1559 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A1416 " --> pdb=" O GLY A1559 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A1561 " --> pdb=" O PHE A1416 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A1418 " --> pdb=" O SER A1561 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A1521 " --> pdb=" O THR A1415 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE A1417 " --> pdb=" O ILE A1521 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN A1523 " --> pdb=" O PHE A1417 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N MET A1419 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1138 through 1142 removed outlier: 7.073A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A1129 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A1113 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE A 961 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET A1115 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY A 963 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS A1008 " --> pdb=" O ILE A1084 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A1086 " --> pdb=" O CYS A1008 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 3.536A pdb=" N VAL A1160 " --> pdb=" O SER A1261 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A1261 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2015 through 2017 removed outlier: 3.560A pdb=" N LEU A2093 " --> pdb=" O GLY A2015 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA A2122 " --> pdb=" O VAL A2092 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A2094 " --> pdb=" O ALA A2122 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A2124 " --> pdb=" O LEU A2094 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2206 through 2209 removed outlier: 3.506A pdb=" N THR A2168 " --> pdb=" O SER A2235 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A2235 " --> pdb=" O THR A2168 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 934 through 936 removed outlier: 3.768A pdb=" N LEU A 934 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 949 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS A 936 " --> pdb=" O ASP A 947 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 947 " --> pdb=" O LYS A 936 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 485 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4935 1.34 - 1.46: 3270 1.46 - 1.58: 7817 1.58 - 1.70: 10 1.70 - 1.82: 139 Bond restraints: 16171 Sorted by residual: bond pdb=" CBV HZL A2311 " pdb=" CBZ HZL A2311 " ideal model delta sigma weight residual 1.345 1.536 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" CAZ HZL A2311 " pdb=" CBD HZL A2311 " ideal model delta sigma weight residual 1.342 1.530 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" CBA HZL A2311 " pdb=" CBE HZL A2311 " ideal model delta sigma weight residual 1.343 1.530 -0.187 2.00e-02 2.50e+03 8.72e+01 bond pdb=" CAN HZL A2311 " pdb=" CAP HZL A2311 " ideal model delta sigma weight residual 1.600 1.417 0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" CAS HZL A2311 " pdb=" CAU HZL A2311 " ideal model delta sigma weight residual 1.350 1.523 -0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.46: 359 105.46 - 112.66: 8567 112.66 - 119.86: 5469 119.86 - 127.06: 7337 127.06 - 134.26: 207 Bond angle restraints: 21939 Sorted by residual: angle pdb=" CAU HZL A2311 " pdb=" CAV HZL A2311 " pdb=" CAW HZL A2311 " ideal model delta sigma weight residual 74.51 121.73 -47.22 3.00e+00 1.11e-01 2.48e+02 angle pdb=" CBR HZL A2311 " pdb=" CBV HZL A2311 " pdb=" CBY HZL A2311 " ideal model delta sigma weight residual 74.50 120.46 -45.96 3.00e+00 1.11e-01 2.35e+02 angle pdb=" CAZ HZL A2311 " pdb=" CBD HZL A2311 " pdb=" CCF HZL A2311 " ideal model delta sigma weight residual 152.65 115.18 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" CBM HZL A2311 " pdb=" CBR HZL A2311 " pdb=" CBV HZL A2311 " ideal model delta sigma weight residual 152.66 119.92 32.74 3.00e+00 1.11e-01 1.19e+02 angle pdb=" CAS HZL A2311 " pdb=" CAU HZL A2311 " pdb=" CAV HZL A2311 " ideal model delta sigma weight residual 85.90 118.27 -32.37 3.00e+00 1.11e-01 1.16e+02 ... (remaining 21934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.63: 9378 33.63 - 67.27: 332 67.27 - 100.90: 24 100.90 - 134.53: 9 134.53 - 168.16: 4 Dihedral angle restraints: 9747 sinusoidal: 3953 harmonic: 5794 Sorted by residual: dihedral pdb=" CA VAL A2197 " pdb=" C VAL A2197 " pdb=" N GLN A2198 " pdb=" CA GLN A2198 " ideal model delta harmonic sigma weight residual 180.00 -135.62 -44.38 0 5.00e+00 4.00e-02 7.88e+01 dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual 93.00 138.58 -45.58 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CA SER A1719 " pdb=" C SER A1719 " pdb=" N PRO A1720 " pdb=" CA PRO A1720 " ideal model delta harmonic sigma weight residual 180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2029 0.058 - 0.116: 446 0.116 - 0.174: 49 0.174 - 0.232: 6 0.232 - 0.290: 7 Chirality restraints: 2537 Sorted by residual: chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3 BMA N 3 " pdb=" C2 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" O3 BMA N 3 " both_signs ideal model delta sigma weight residual False 2.41 2.12 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2534 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1963 " 0.047 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A1964 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1964 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1964 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1546 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C LEU A1546 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU A1546 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A1547 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 980 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A 981 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 981 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 981 " 0.033 5.00e-02 4.00e+02 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 98 2.58 - 3.16: 13265 3.16 - 3.74: 22131 3.74 - 4.32: 30516 4.32 - 4.90: 51435 Nonbonded interactions: 117445 Sorted by model distance: nonbonded pdb=" OG1 THR A1019 " pdb=" OE1 GLU A1022 " model vdw 2.006 2.440 nonbonded pdb=" OG SER A1034 " pdb=" OE1 GLU A1037 " model vdw 2.073 2.440 nonbonded pdb=" O VAL A1718 " pdb=" OG1 THR A1722 " model vdw 2.137 2.440 nonbonded pdb=" OG SER A2072 " pdb=" OD1 ASN A2075 " model vdw 2.198 2.440 nonbonded pdb=" CA GLY A1154 " pdb=" O LEU A1233 " model vdw 2.213 3.440 ... (remaining 117440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.780 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 43.430 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.008 0.191 16171 Z= 0.484 Angle : 1.105 47.224 21939 Z= 0.529 Chirality : 0.050 0.290 2537 Planarity : 0.005 0.068 2747 Dihedral : 17.002 168.164 5983 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.99 % Favored : 87.35 % Rotamer: Outliers : 2.13 % Allowed : 1.26 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.17), residues: 1977 helix: -1.33 (0.16), residues: 987 sheet: -2.47 (0.35), residues: 179 loop : -3.68 (0.18), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1449 HIS 0.006 0.001 HIS A2032 PHE 0.030 0.002 PHE A1440 TYR 0.027 0.002 TYR A1139 ARG 0.011 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 1.934 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 233 average time/residue: 0.2936 time to fit residues: 103.3247 Evaluate side-chains 187 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2518 time to fit residues: 8.2194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 964 HIS A2032 HIS ** A2052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16171 Z= 0.291 Angle : 0.818 24.117 21939 Z= 0.379 Chirality : 0.047 0.300 2537 Planarity : 0.005 0.060 2747 Dihedral : 14.084 170.311 2558 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.28 % Favored : 88.52 % Rotamer: Outliers : 1.26 % Allowed : 9.48 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.18), residues: 1977 helix: -0.99 (0.17), residues: 964 sheet: -2.26 (0.38), residues: 163 loop : -3.57 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 925 HIS 0.004 0.001 HIS A1608 PHE 0.025 0.001 PHE A1146 TYR 0.023 0.002 TYR A 400 ARG 0.006 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.879 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 203 average time/residue: 0.2931 time to fit residues: 90.0947 Evaluate side-chains 186 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1590 time to fit residues: 5.7197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 151 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 145 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 447 GLN ** A2052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 GLN ** A2243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16171 Z= 0.161 Angle : 0.727 24.669 21939 Z= 0.331 Chirality : 0.043 0.278 2537 Planarity : 0.004 0.059 2747 Dihedral : 13.392 177.543 2558 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.02 % Favored : 89.83 % Rotamer: Outliers : 0.82 % Allowed : 13.62 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.18), residues: 1977 helix: -0.60 (0.17), residues: 975 sheet: -1.87 (0.39), residues: 158 loop : -3.43 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 925 HIS 0.003 0.000 HIS A 130 PHE 0.022 0.001 PHE A1146 TYR 0.019 0.001 TYR A 345 ARG 0.006 0.000 ARG A1443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3954 Ramachandran restraints generated. 1977 Oldfield, 0 Emsley, 1977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 1.845 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 215 average time/residue: 0.2943 time to fit residues: 94.2472 Evaluate side-chains 193 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1445 time to fit residues: 3.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2725 > 50: distance: 26 - 31: 4.244 distance: 31 - 32: 10.791 distance: 32 - 33: 15.771 distance: 33 - 34: 9.735 distance: 33 - 35: 6.021 distance: 35 - 36: 8.177 distance: 36 - 37: 11.589 distance: 36 - 39: 12.754 distance: 37 - 38: 13.417 distance: 37 - 44: 15.930 distance: 39 - 40: 3.547 distance: 40 - 41: 14.787 distance: 41 - 42: 6.252 distance: 41 - 43: 7.442 distance: 45 - 46: 4.953 distance: 45 - 48: 18.516 distance: 46 - 47: 5.525 distance: 46 - 50: 7.016 distance: 48 - 49: 10.762 distance: 50 - 51: 5.414 distance: 51 - 52: 6.411 distance: 51 - 54: 6.691 distance: 52 - 53: 7.789 distance: 52 - 61: 5.208 distance: 54 - 55: 8.193 distance: 55 - 56: 4.653 distance: 55 - 57: 8.299 distance: 56 - 58: 3.772 distance: 57 - 59: 10.730 distance: 58 - 60: 8.628 distance: 59 - 60: 8.566 distance: 61 - 62: 9.206 distance: 62 - 63: 7.776 distance: 63 - 64: 12.152 distance: 63 - 65: 6.397 distance: 66 - 67: 13.245 distance: 66 - 69: 20.205 distance: 67 - 68: 7.952 distance: 67 - 73: 6.105 distance: 69 - 70: 14.380 distance: 70 - 71: 15.444 distance: 70 - 72: 23.585 distance: 73 - 74: 5.920 distance: 74 - 77: 10.049 distance: 75 - 76: 35.453 distance: 75 - 81: 11.575 distance: 77 - 78: 12.454 distance: 78 - 79: 19.403 distance: 78 - 80: 9.098 distance: 81 - 82: 11.713 distance: 82 - 83: 13.175 distance: 83 - 84: 36.739 distance: 83 - 85: 28.573 distance: 85 - 86: 9.263 distance: 86 - 87: 18.891 distance: 86 - 89: 15.670 distance: 87 - 88: 10.932 distance: 87 - 92: 12.108 distance: 89 - 90: 28.518 distance: 89 - 91: 20.342 distance: 92 - 93: 3.663 distance: 93 - 94: 16.379 distance: 93 - 96: 4.508 distance: 94 - 95: 17.534 distance: 94 - 100: 18.286 distance: 96 - 97: 10.825 distance: 97 - 99: 15.396