Starting phenix.real_space_refine on Sun Feb 18 05:18:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5v_31468/02_2024/7f5v_31468.pdb" } resolution = 3.6 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= 0.002 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13116 2.51 5 N 3688 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 683": "OD1" <-> "OD2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 683": "OD1" <-> "OD2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ARG 330": "NH1" <-> "NH2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 683": "OD1" <-> "OD2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 608": "OE1" <-> "OE2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 683": "OD1" <-> "OD2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 10.98, per 1000 atoms: 0.53 Number of scatterers: 20912 At special positions: 0 Unit cell: (193.98, 98.58, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3988 8.00 N 3688 7.00 C 13116 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: 8.68 Conformation dependent library (CDL) restraints added in 4.1 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 47.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 55 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 55 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 93 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER C 612 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 55 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY D 425 " --> pdb=" O ASN D 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 513 Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER D 612 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 638 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET A 100 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR A 205 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR A 102 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 101 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 61 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET A 252 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 62 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 315 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 251 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU A 450 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 452 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 443 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN A 454 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU A 487 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 464 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE A 606 " --> pdb=" O GLU A 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY A 736 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET B 100 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR B 205 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR B 102 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 101 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 61 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET B 252 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 62 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS B 315 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 251 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU B 450 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG B 445 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 452 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG B 443 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN B 454 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU B 487 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 464 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE B 606 " --> pdb=" O GLU B 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY B 736 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET C 100 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR C 205 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR C 102 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 101 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 61 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET C 252 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 62 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 315 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 251 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU C 450 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 445 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 452 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG C 443 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN C 454 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU C 487 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 464 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE C 606 " --> pdb=" O GLU C 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY C 736 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET D 100 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR D 205 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR D 102 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL D 101 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 61 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET D 252 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS D 62 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS D 315 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 251 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU D 450 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG D 445 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU D 452 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 443 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN D 454 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU D 487 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 464 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE D 606 " --> pdb=" O GLU D 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY D 736 " --> pdb=" O SER D 728 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2544 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: 6.59 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7136 1.34 - 1.46: 3988 1.46 - 1.58: 9896 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 21220 Sorted by residual: bond pdb=" C GLY C 165 " pdb=" N VAL C 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY B 165 " pdb=" N VAL B 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY D 165 " pdb=" N VAL D 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" CG ARG C 544 " pdb=" CD ARG C 544 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 21215 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.19: 524 106.19 - 113.15: 12124 113.15 - 120.11: 7064 120.11 - 127.07: 8804 127.07 - 134.03: 196 Bond angle restraints: 28712 Sorted by residual: angle pdb=" N VAL A 725 " pdb=" CA VAL A 725 " pdb=" C VAL A 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL D 725 " pdb=" CA VAL D 725 " pdb=" C VAL D 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL C 725 " pdb=" CA VAL C 725 " pdb=" C VAL C 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL B 725 " pdb=" CA VAL B 725 " pdb=" C VAL B 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ALA B 339 " pdb=" CA ALA B 339 " pdb=" C ALA B 339 " ideal model delta sigma weight residual 111.75 115.86 -4.11 1.28e+00 6.10e-01 1.03e+01 ... (remaining 28707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11392 15.07 - 30.14: 1228 30.14 - 45.20: 296 45.20 - 60.27: 52 60.27 - 75.34: 32 Dihedral angle restraints: 13000 sinusoidal: 5068 harmonic: 7932 Sorted by residual: dihedral pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" N GLU D 349 " pdb=" CA GLU D 349 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL C 348 " pdb=" C VAL C 348 " pdb=" N GLU C 349 " pdb=" CA GLU C 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N GLU A 349 " pdb=" CA GLU A 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1960 0.031 - 0.062: 944 0.062 - 0.092: 280 0.092 - 0.123: 176 0.123 - 0.154: 28 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA PRO C 347 " pdb=" N PRO C 347 " pdb=" C PRO C 347 " pdb=" CB PRO C 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO A 347 " pdb=" N PRO A 347 " pdb=" C PRO A 347 " pdb=" CB PRO A 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO D 347 " pdb=" N PRO D 347 " pdb=" C PRO D 347 " pdb=" CB PRO D 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 3385 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 643 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 644 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 644 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 644 " 0.028 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 408 2.64 - 3.21: 21410 3.21 - 3.77: 31480 3.77 - 4.34: 43910 4.34 - 4.90: 69802 Nonbonded interactions: 167010 Sorted by model distance: nonbonded pdb=" OG1 THR C 687 " pdb=" OD1 ASN C 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR B 687 " pdb=" OD1 ASN B 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 689 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR D 687 " pdb=" OD1 ASN D 689 " model vdw 2.076 2.440 nonbonded pdb=" OG SER C 546 " pdb=" OD1 ASP C 548 " model vdw 2.150 2.440 ... (remaining 167005 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 56.420 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.120 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.005 0.035 21220 Z= 0.322 Angle : 0.687 6.442 28712 Z= 0.413 Chirality : 0.044 0.154 3388 Planarity : 0.005 0.052 3720 Dihedral : 13.935 75.336 7856 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 0.18 % Allowed : 5.88 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.13), residues: 2728 helix: -2.60 (0.12), residues: 1108 sheet: -3.38 (0.20), residues: 448 loop : -3.40 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 748 HIS 0.005 0.001 HIS A 707 PHE 0.006 0.001 PHE D 108 TYR 0.009 0.001 TYR D 631 ARG 0.003 0.000 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASP cc_start: 0.8327 (t0) cc_final: 0.8091 (t0) REVERT: A 177 ASP cc_start: 0.7548 (m-30) cc_final: 0.7182 (m-30) REVERT: A 234 ASP cc_start: 0.8559 (t0) cc_final: 0.8336 (t0) REVERT: A 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8585 (mmm) REVERT: B 158 ASP cc_start: 0.8326 (t0) cc_final: 0.8090 (t0) REVERT: B 177 ASP cc_start: 0.7549 (m-30) cc_final: 0.7183 (m-30) REVERT: B 234 ASP cc_start: 0.8559 (t0) cc_final: 0.8338 (t0) REVERT: B 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8585 (mmm) REVERT: C 158 ASP cc_start: 0.8331 (t0) cc_final: 0.8092 (t0) REVERT: C 177 ASP cc_start: 0.7548 (m-30) cc_final: 0.7183 (m-30) REVERT: C 234 ASP cc_start: 0.8558 (t0) cc_final: 0.8337 (t0) REVERT: C 622 MET cc_start: 0.8940 (tpt) cc_final: 0.8586 (mmm) REVERT: D 158 ASP cc_start: 0.8330 (t0) cc_final: 0.8092 (t0) REVERT: D 177 ASP cc_start: 0.7549 (m-30) cc_final: 0.7183 (m-30) REVERT: D 234 ASP cc_start: 0.8558 (t0) cc_final: 0.8337 (t0) REVERT: D 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8587 (mmm) outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.3378 time to fit residues: 151.8220 Evaluate side-chains 216 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 250 optimal weight: 0.0370 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 369 GLN A 375 ASN A 392 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 675 HIS B 344 ASN B 369 GLN B 375 ASN B 392 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 675 HIS C 344 ASN C 369 GLN C 375 ASN C 392 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 675 HIS D 344 ASN D 369 GLN D 375 ASN D 392 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 HIS D 675 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21220 Z= 0.188 Angle : 0.595 7.370 28712 Z= 0.311 Chirality : 0.044 0.190 3388 Planarity : 0.004 0.045 3720 Dihedral : 4.415 21.724 2932 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.99 % Rotamer: Outliers : 1.96 % Allowed : 12.48 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2728 helix: -0.69 (0.14), residues: 1172 sheet: -2.57 (0.23), residues: 420 loop : -2.88 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 748 HIS 0.006 0.001 HIS D 559 PHE 0.011 0.001 PHE B 335 TYR 0.011 0.001 TYR B 594 ARG 0.003 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8465 (tp30) cc_final: 0.8211 (tp30) REVERT: A 158 ASP cc_start: 0.8154 (t0) cc_final: 0.7913 (t0) REVERT: A 213 MET cc_start: 0.7227 (mmm) cc_final: 0.6953 (mmm) REVERT: A 234 ASP cc_start: 0.8370 (t0) cc_final: 0.8114 (t0) REVERT: A 324 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8822 (ttmt) REVERT: A 392 ASN cc_start: 0.4319 (OUTLIER) cc_final: 0.3895 (t0) REVERT: A 503 MET cc_start: 0.5965 (tpp) cc_final: 0.5700 (tpp) REVERT: A 622 MET cc_start: 0.8848 (tpt) cc_final: 0.8566 (mmm) REVERT: A 704 CYS cc_start: 0.8110 (p) cc_final: 0.7273 (p) REVERT: A 715 ASP cc_start: 0.6673 (t0) cc_final: 0.5969 (t0) REVERT: A 760 PHE cc_start: 0.6902 (m-80) cc_final: 0.6566 (m-80) REVERT: B 49 GLU cc_start: 0.8464 (tp30) cc_final: 0.8210 (tp30) REVERT: B 158 ASP cc_start: 0.8154 (t0) cc_final: 0.7916 (t0) REVERT: B 213 MET cc_start: 0.7229 (mmm) cc_final: 0.6957 (mmm) REVERT: B 234 ASP cc_start: 0.8369 (t0) cc_final: 0.8116 (t0) REVERT: B 324 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8822 (ttmt) REVERT: B 392 ASN cc_start: 0.4314 (OUTLIER) cc_final: 0.3886 (t0) REVERT: B 503 MET cc_start: 0.5964 (tpp) cc_final: 0.5701 (tpp) REVERT: B 622 MET cc_start: 0.8843 (tpt) cc_final: 0.8565 (mmm) REVERT: B 704 CYS cc_start: 0.8115 (p) cc_final: 0.7281 (p) REVERT: B 715 ASP cc_start: 0.6668 (t0) cc_final: 0.5965 (t0) REVERT: B 760 PHE cc_start: 0.6897 (m-80) cc_final: 0.6563 (m-80) REVERT: C 49 GLU cc_start: 0.8465 (tp30) cc_final: 0.8212 (tp30) REVERT: C 158 ASP cc_start: 0.8155 (t0) cc_final: 0.7914 (t0) REVERT: C 213 MET cc_start: 0.7228 (mmm) cc_final: 0.6956 (mmm) REVERT: C 234 ASP cc_start: 0.8368 (t0) cc_final: 0.8112 (t0) REVERT: C 324 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8823 (ttmt) REVERT: C 392 ASN cc_start: 0.4318 (OUTLIER) cc_final: 0.3892 (t0) REVERT: C 503 MET cc_start: 0.5957 (tpp) cc_final: 0.5696 (tpp) REVERT: C 622 MET cc_start: 0.8845 (tpt) cc_final: 0.8566 (mmm) REVERT: C 704 CYS cc_start: 0.8115 (p) cc_final: 0.7271 (p) REVERT: C 715 ASP cc_start: 0.6674 (t0) cc_final: 0.5966 (t0) REVERT: C 760 PHE cc_start: 0.6896 (m-80) cc_final: 0.6563 (m-80) REVERT: D 49 GLU cc_start: 0.8464 (tp30) cc_final: 0.8212 (tp30) REVERT: D 158 ASP cc_start: 0.8155 (t0) cc_final: 0.7918 (t0) REVERT: D 213 MET cc_start: 0.7229 (mmm) cc_final: 0.6956 (mmm) REVERT: D 234 ASP cc_start: 0.8371 (t0) cc_final: 0.8113 (t0) REVERT: D 324 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8821 (ttmt) REVERT: D 392 ASN cc_start: 0.4315 (OUTLIER) cc_final: 0.3888 (t0) REVERT: D 503 MET cc_start: 0.5957 (tpp) cc_final: 0.5695 (tpp) REVERT: D 622 MET cc_start: 0.8845 (tpt) cc_final: 0.8566 (mmm) REVERT: D 704 CYS cc_start: 0.8113 (p) cc_final: 0.7272 (p) REVERT: D 715 ASP cc_start: 0.6667 (t0) cc_final: 0.5963 (t0) REVERT: D 760 PHE cc_start: 0.6895 (m-80) cc_final: 0.6562 (m-80) outliers start: 44 outliers final: 16 residues processed: 300 average time/residue: 0.2767 time to fit residues: 134.5503 Evaluate side-chains 268 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 392 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 392 ASN A 454 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 392 ASN B 454 GLN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN C 344 ASN C 392 ASN C 454 GLN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 392 ASN D 454 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21220 Z= 0.186 Angle : 0.563 11.145 28712 Z= 0.288 Chirality : 0.043 0.159 3388 Planarity : 0.004 0.044 3720 Dihedral : 4.249 20.123 2932 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 2.14 % Allowed : 16.04 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2728 helix: 0.06 (0.15), residues: 1172 sheet: -2.35 (0.24), residues: 444 loop : -2.52 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 748 HIS 0.007 0.001 HIS C 673 PHE 0.011 0.001 PHE D 336 TYR 0.008 0.001 TYR A 274 ARG 0.001 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 268 time to evaluate : 2.645 Fit side-chains REVERT: A 158 ASP cc_start: 0.8158 (t0) cc_final: 0.7956 (t0) REVERT: A 234 ASP cc_start: 0.8353 (t0) cc_final: 0.8081 (t0) REVERT: A 344 ASN cc_start: 0.2669 (OUTLIER) cc_final: 0.1296 (t0) REVERT: A 622 MET cc_start: 0.8921 (tpt) cc_final: 0.8625 (mmm) REVERT: A 704 CYS cc_start: 0.8148 (p) cc_final: 0.7343 (p) REVERT: A 760 PHE cc_start: 0.6965 (m-80) cc_final: 0.6568 (m-80) REVERT: B 234 ASP cc_start: 0.8356 (t0) cc_final: 0.8085 (t0) REVERT: B 344 ASN cc_start: 0.2672 (OUTLIER) cc_final: 0.1301 (t0) REVERT: B 622 MET cc_start: 0.8922 (tpt) cc_final: 0.8625 (mmm) REVERT: B 704 CYS cc_start: 0.8148 (p) cc_final: 0.7349 (p) REVERT: B 760 PHE cc_start: 0.6964 (m-80) cc_final: 0.6563 (m-80) REVERT: C 158 ASP cc_start: 0.8157 (t0) cc_final: 0.7956 (t0) REVERT: C 234 ASP cc_start: 0.8351 (t0) cc_final: 0.8077 (t0) REVERT: C 344 ASN cc_start: 0.2672 (OUTLIER) cc_final: 0.1297 (t0) REVERT: C 622 MET cc_start: 0.8923 (tpt) cc_final: 0.8626 (mmm) REVERT: C 704 CYS cc_start: 0.8150 (p) cc_final: 0.7345 (p) REVERT: C 760 PHE cc_start: 0.6964 (m-80) cc_final: 0.6567 (m-80) REVERT: D 234 ASP cc_start: 0.8353 (t0) cc_final: 0.8081 (t0) REVERT: D 344 ASN cc_start: 0.2672 (OUTLIER) cc_final: 0.1299 (t0) REVERT: D 622 MET cc_start: 0.8922 (tpt) cc_final: 0.8624 (mmm) REVERT: D 704 CYS cc_start: 0.8146 (p) cc_final: 0.7341 (p) REVERT: D 760 PHE cc_start: 0.6961 (m-80) cc_final: 0.6564 (m-80) outliers start: 48 outliers final: 24 residues processed: 304 average time/residue: 0.2841 time to fit residues: 140.6673 Evaluate side-chains 264 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 238 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 565 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN B 344 ASN B 565 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 565 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 565 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21220 Z= 0.357 Angle : 0.629 8.669 28712 Z= 0.324 Chirality : 0.044 0.177 3388 Planarity : 0.005 0.069 3720 Dihedral : 4.582 21.980 2932 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.62 % Favored : 92.23 % Rotamer: Outliers : 2.67 % Allowed : 17.83 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2728 helix: 0.19 (0.15), residues: 1176 sheet: -2.28 (0.25), residues: 384 loop : -2.57 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 748 HIS 0.006 0.001 HIS C 673 PHE 0.012 0.002 PHE D 336 TYR 0.007 0.001 TYR A 274 ARG 0.002 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8483 (t0) cc_final: 0.8208 (t0) REVERT: A 601 MET cc_start: 0.7444 (tmm) cc_final: 0.6288 (tmm) REVERT: A 622 MET cc_start: 0.8901 (tpt) cc_final: 0.8593 (mmm) REVERT: A 704 CYS cc_start: 0.8091 (p) cc_final: 0.7279 (p) REVERT: A 715 ASP cc_start: 0.6481 (t0) cc_final: 0.5555 (t0) REVERT: A 760 PHE cc_start: 0.7050 (m-80) cc_final: 0.6572 (m-80) REVERT: B 234 ASP cc_start: 0.8479 (t0) cc_final: 0.8208 (t0) REVERT: B 601 MET cc_start: 0.7442 (tmm) cc_final: 0.6291 (tmm) REVERT: B 622 MET cc_start: 0.8898 (tpt) cc_final: 0.8592 (mmm) REVERT: B 704 CYS cc_start: 0.8089 (p) cc_final: 0.7282 (p) REVERT: B 715 ASP cc_start: 0.6480 (t0) cc_final: 0.5559 (t0) REVERT: B 760 PHE cc_start: 0.7049 (m-80) cc_final: 0.6572 (m-80) REVERT: C 234 ASP cc_start: 0.8477 (t0) cc_final: 0.8203 (t0) REVERT: C 534 MET cc_start: 0.6711 (ttp) cc_final: 0.6293 (tmm) REVERT: C 601 MET cc_start: 0.7442 (tmm) cc_final: 0.6287 (tmm) REVERT: C 622 MET cc_start: 0.8898 (tpt) cc_final: 0.8593 (mmm) REVERT: C 704 CYS cc_start: 0.8085 (p) cc_final: 0.7274 (p) REVERT: C 715 ASP cc_start: 0.6483 (t0) cc_final: 0.5555 (t0) REVERT: C 760 PHE cc_start: 0.7049 (m-80) cc_final: 0.6572 (m-80) REVERT: D 234 ASP cc_start: 0.8476 (t0) cc_final: 0.8207 (t0) REVERT: D 601 MET cc_start: 0.7443 (tmm) cc_final: 0.6289 (tmm) REVERT: D 622 MET cc_start: 0.8900 (tpt) cc_final: 0.8593 (mmm) REVERT: D 704 CYS cc_start: 0.8080 (p) cc_final: 0.7272 (p) REVERT: D 715 ASP cc_start: 0.6477 (t0) cc_final: 0.5554 (t0) REVERT: D 760 PHE cc_start: 0.7052 (m-80) cc_final: 0.6575 (m-80) outliers start: 60 outliers final: 36 residues processed: 270 average time/residue: 0.2730 time to fit residues: 122.4841 Evaluate side-chains 248 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 136 optimal weight: 30.0000 chunk 239 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 21220 Z= 0.394 Angle : 0.644 7.138 28712 Z= 0.334 Chirality : 0.045 0.152 3388 Planarity : 0.005 0.064 3720 Dihedral : 4.670 19.602 2932 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 2.85 % Allowed : 18.85 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2728 helix: 0.10 (0.15), residues: 1180 sheet: -2.26 (0.26), residues: 380 loop : -2.58 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 768 HIS 0.005 0.001 HIS A 707 PHE 0.012 0.002 PHE C 335 TYR 0.009 0.001 TYR A 274 ARG 0.003 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 208 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8575 (tpp) cc_final: 0.8187 (tmm) REVERT: A 234 ASP cc_start: 0.8454 (t0) cc_final: 0.8205 (t0) REVERT: A 503 MET cc_start: 0.6790 (tpp) cc_final: 0.6017 (tpp) REVERT: A 601 MET cc_start: 0.7294 (tmm) cc_final: 0.6299 (tmm) REVERT: A 622 MET cc_start: 0.8924 (tpt) cc_final: 0.8597 (mmm) REVERT: A 704 CYS cc_start: 0.8049 (p) cc_final: 0.7193 (p) REVERT: A 760 PHE cc_start: 0.7203 (m-80) cc_final: 0.6661 (m-80) REVERT: B 119 MET cc_start: 0.8575 (tpp) cc_final: 0.8189 (tmm) REVERT: B 234 ASP cc_start: 0.8453 (t0) cc_final: 0.8207 (t0) REVERT: B 503 MET cc_start: 0.6783 (tpp) cc_final: 0.6011 (tpp) REVERT: B 601 MET cc_start: 0.7295 (tmm) cc_final: 0.6303 (tmm) REVERT: B 622 MET cc_start: 0.8922 (tpt) cc_final: 0.8596 (mmm) REVERT: B 704 CYS cc_start: 0.8055 (p) cc_final: 0.7196 (p) REVERT: B 760 PHE cc_start: 0.7202 (m-80) cc_final: 0.6659 (m-80) REVERT: C 119 MET cc_start: 0.8575 (tpp) cc_final: 0.8187 (tmm) REVERT: C 234 ASP cc_start: 0.8450 (t0) cc_final: 0.8202 (t0) REVERT: C 503 MET cc_start: 0.6787 (tpp) cc_final: 0.6012 (tpp) REVERT: C 601 MET cc_start: 0.7291 (tmm) cc_final: 0.6301 (tmm) REVERT: C 622 MET cc_start: 0.8922 (tpt) cc_final: 0.8595 (mmm) REVERT: C 704 CYS cc_start: 0.8049 (p) cc_final: 0.7190 (p) REVERT: C 760 PHE cc_start: 0.7202 (m-80) cc_final: 0.6660 (m-80) REVERT: D 119 MET cc_start: 0.8575 (tpp) cc_final: 0.8187 (tmm) REVERT: D 234 ASP cc_start: 0.8450 (t0) cc_final: 0.8193 (t0) REVERT: D 503 MET cc_start: 0.6785 (tpp) cc_final: 0.6012 (tpp) REVERT: D 601 MET cc_start: 0.7298 (tmm) cc_final: 0.6306 (tmm) REVERT: D 622 MET cc_start: 0.8923 (tpt) cc_final: 0.8596 (mmm) REVERT: D 704 CYS cc_start: 0.8050 (p) cc_final: 0.7193 (p) REVERT: D 760 PHE cc_start: 0.7206 (m-80) cc_final: 0.6663 (m-80) outliers start: 64 outliers final: 40 residues processed: 248 average time/residue: 0.2804 time to fit residues: 114.0009 Evaluate side-chains 248 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 0.0870 chunk 65 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.240 Angle : 0.567 6.484 28712 Z= 0.297 Chirality : 0.043 0.149 3388 Planarity : 0.004 0.051 3720 Dihedral : 4.384 17.759 2932 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.26 % Rotamer: Outliers : 2.14 % Allowed : 19.16 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2728 helix: 0.19 (0.15), residues: 1208 sheet: -2.14 (0.26), residues: 380 loop : -2.36 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 748 HIS 0.005 0.001 HIS B 673 PHE 0.010 0.001 PHE B 335 TYR 0.005 0.001 TYR B 274 ARG 0.002 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 254 time to evaluate : 2.343 Fit side-chains REVERT: A 119 MET cc_start: 0.8484 (tpp) cc_final: 0.8228 (tmm) REVERT: A 601 MET cc_start: 0.7257 (tmm) cc_final: 0.6269 (tmm) REVERT: A 622 MET cc_start: 0.8918 (tpt) cc_final: 0.8619 (mmm) REVERT: A 669 GLU cc_start: 0.7293 (pt0) cc_final: 0.6916 (tp30) REVERT: A 704 CYS cc_start: 0.8061 (p) cc_final: 0.7181 (p) REVERT: A 715 ASP cc_start: 0.6338 (t0) cc_final: 0.5265 (t0) REVERT: A 760 PHE cc_start: 0.7103 (m-80) cc_final: 0.6560 (m-80) REVERT: B 119 MET cc_start: 0.8484 (tpp) cc_final: 0.8224 (tmm) REVERT: B 601 MET cc_start: 0.7260 (tmm) cc_final: 0.6268 (tmm) REVERT: B 622 MET cc_start: 0.8918 (tpt) cc_final: 0.8619 (mmm) REVERT: B 669 GLU cc_start: 0.7293 (pt0) cc_final: 0.6921 (tp30) REVERT: B 704 CYS cc_start: 0.8064 (p) cc_final: 0.7187 (p) REVERT: B 715 ASP cc_start: 0.6336 (t0) cc_final: 0.5268 (t0) REVERT: B 760 PHE cc_start: 0.7103 (m-80) cc_final: 0.6559 (m-80) REVERT: C 119 MET cc_start: 0.8482 (tpp) cc_final: 0.8221 (tmm) REVERT: C 601 MET cc_start: 0.7256 (tmm) cc_final: 0.6266 (tmm) REVERT: C 622 MET cc_start: 0.8918 (tpt) cc_final: 0.8620 (mmm) REVERT: C 669 GLU cc_start: 0.7292 (pt0) cc_final: 0.6916 (tp30) REVERT: C 704 CYS cc_start: 0.8058 (p) cc_final: 0.7176 (p) REVERT: C 715 ASP cc_start: 0.6338 (t0) cc_final: 0.5261 (t0) REVERT: C 760 PHE cc_start: 0.7105 (m-80) cc_final: 0.6561 (m-80) REVERT: D 119 MET cc_start: 0.8484 (tpp) cc_final: 0.8225 (tmm) REVERT: D 601 MET cc_start: 0.7260 (tmm) cc_final: 0.6267 (tmm) REVERT: D 622 MET cc_start: 0.8919 (tpt) cc_final: 0.8620 (mmm) REVERT: D 669 GLU cc_start: 0.7294 (pt0) cc_final: 0.6920 (tp30) REVERT: D 704 CYS cc_start: 0.8057 (p) cc_final: 0.7178 (p) REVERT: D 715 ASP cc_start: 0.6337 (t0) cc_final: 0.5262 (t0) REVERT: D 760 PHE cc_start: 0.7104 (m-80) cc_final: 0.6559 (m-80) outliers start: 48 outliers final: 32 residues processed: 290 average time/residue: 0.2772 time to fit residues: 132.0527 Evaluate side-chains 272 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 HIS ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21220 Z= 0.225 Angle : 0.581 7.988 28712 Z= 0.299 Chirality : 0.043 0.155 3388 Planarity : 0.004 0.046 3720 Dihedral : 4.239 17.468 2932 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 2.14 % Allowed : 20.32 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.17), residues: 2728 helix: 0.42 (0.16), residues: 1204 sheet: -2.03 (0.26), residues: 380 loop : -2.31 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 748 HIS 0.007 0.001 HIS A 673 PHE 0.010 0.001 PHE D 335 TYR 0.005 0.001 TYR B 164 ARG 0.003 0.000 ARG C 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 2.455 Fit side-chains REVERT: A 119 MET cc_start: 0.8494 (tpp) cc_final: 0.8223 (tmm) REVERT: A 481 MET cc_start: 0.7530 (ptt) cc_final: 0.7133 (tpt) REVERT: A 503 MET cc_start: 0.6922 (tpp) cc_final: 0.5876 (mpp) REVERT: A 622 MET cc_start: 0.8914 (tpt) cc_final: 0.8637 (mmm) REVERT: A 669 GLU cc_start: 0.7471 (pt0) cc_final: 0.7204 (tp30) REVERT: A 704 CYS cc_start: 0.7972 (p) cc_final: 0.7105 (p) REVERT: A 715 ASP cc_start: 0.6371 (t0) cc_final: 0.5341 (t0) REVERT: A 760 PHE cc_start: 0.7096 (m-80) cc_final: 0.6609 (m-80) REVERT: B 119 MET cc_start: 0.8494 (tpp) cc_final: 0.8226 (tmm) REVERT: B 481 MET cc_start: 0.7531 (ptt) cc_final: 0.7136 (tpt) REVERT: B 503 MET cc_start: 0.6918 (tpp) cc_final: 0.5873 (mpp) REVERT: B 622 MET cc_start: 0.8915 (tpt) cc_final: 0.8637 (mmm) REVERT: B 669 GLU cc_start: 0.7467 (pt0) cc_final: 0.7202 (tp30) REVERT: B 704 CYS cc_start: 0.7974 (p) cc_final: 0.7108 (p) REVERT: B 715 ASP cc_start: 0.6364 (t0) cc_final: 0.5336 (t0) REVERT: B 760 PHE cc_start: 0.7098 (m-80) cc_final: 0.6612 (m-80) REVERT: C 119 MET cc_start: 0.8495 (tpp) cc_final: 0.8223 (tmm) REVERT: C 481 MET cc_start: 0.7528 (ptt) cc_final: 0.7122 (tpt) REVERT: C 503 MET cc_start: 0.6925 (tpp) cc_final: 0.5880 (mpp) REVERT: C 622 MET cc_start: 0.8915 (tpt) cc_final: 0.8638 (mmm) REVERT: C 669 GLU cc_start: 0.7469 (pt0) cc_final: 0.7199 (tp30) REVERT: C 704 CYS cc_start: 0.7968 (p) cc_final: 0.7099 (p) REVERT: C 715 ASP cc_start: 0.6365 (t0) cc_final: 0.5335 (t0) REVERT: C 760 PHE cc_start: 0.7092 (m-80) cc_final: 0.6608 (m-80) REVERT: D 119 MET cc_start: 0.8496 (tpp) cc_final: 0.8226 (tmm) REVERT: D 481 MET cc_start: 0.7531 (ptt) cc_final: 0.7136 (tpt) REVERT: D 503 MET cc_start: 0.6920 (tpp) cc_final: 0.5874 (mpp) REVERT: D 622 MET cc_start: 0.8915 (tpt) cc_final: 0.8637 (mmm) REVERT: D 669 GLU cc_start: 0.7467 (pt0) cc_final: 0.7201 (tp30) REVERT: D 704 CYS cc_start: 0.7971 (p) cc_final: 0.7103 (p) REVERT: D 715 ASP cc_start: 0.6367 (t0) cc_final: 0.5338 (t0) REVERT: D 760 PHE cc_start: 0.7098 (m-80) cc_final: 0.6611 (m-80) outliers start: 48 outliers final: 40 residues processed: 290 average time/residue: 0.2798 time to fit residues: 131.4534 Evaluate side-chains 290 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 169 optimal weight: 0.0020 chunk 181 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21220 Z= 0.207 Angle : 0.580 7.698 28712 Z= 0.295 Chirality : 0.043 0.143 3388 Planarity : 0.004 0.044 3720 Dihedral : 4.137 17.278 2932 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 2.14 % Allowed : 21.66 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2728 helix: 0.49 (0.16), residues: 1212 sheet: -1.91 (0.24), residues: 432 loop : -2.21 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 748 HIS 0.003 0.001 HIS B 92 PHE 0.010 0.001 PHE D 335 TYR 0.007 0.001 TYR A 631 ARG 0.005 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8478 (tpp) cc_final: 0.8207 (tmm) REVERT: A 503 MET cc_start: 0.6900 (tpp) cc_final: 0.5956 (tpp) REVERT: A 601 MET cc_start: 0.7724 (tmm) cc_final: 0.7116 (tmm) REVERT: A 622 MET cc_start: 0.8893 (tpt) cc_final: 0.8635 (mmm) REVERT: A 704 CYS cc_start: 0.7964 (p) cc_final: 0.7095 (p) REVERT: A 715 ASP cc_start: 0.6401 (t0) cc_final: 0.5415 (t0) REVERT: A 760 PHE cc_start: 0.7066 (m-80) cc_final: 0.6565 (m-80) REVERT: B 119 MET cc_start: 0.8483 (tpp) cc_final: 0.8215 (tmm) REVERT: B 503 MET cc_start: 0.6893 (tpp) cc_final: 0.5952 (tpp) REVERT: B 601 MET cc_start: 0.7724 (tmm) cc_final: 0.7115 (tmm) REVERT: B 622 MET cc_start: 0.8895 (tpt) cc_final: 0.8636 (mmm) REVERT: B 704 CYS cc_start: 0.7960 (p) cc_final: 0.7097 (p) REVERT: B 715 ASP cc_start: 0.6401 (t0) cc_final: 0.5419 (t0) REVERT: B 760 PHE cc_start: 0.7068 (m-80) cc_final: 0.6568 (m-80) REVERT: C 119 MET cc_start: 0.8483 (tpp) cc_final: 0.8216 (tmm) REVERT: C 503 MET cc_start: 0.6901 (tpp) cc_final: 0.5957 (tpp) REVERT: C 601 MET cc_start: 0.7724 (tmm) cc_final: 0.7115 (tmm) REVERT: C 622 MET cc_start: 0.8893 (tpt) cc_final: 0.8636 (mmm) REVERT: C 704 CYS cc_start: 0.7961 (p) cc_final: 0.7096 (p) REVERT: C 715 ASP cc_start: 0.6397 (t0) cc_final: 0.5414 (t0) REVERT: C 760 PHE cc_start: 0.7064 (m-80) cc_final: 0.6565 (m-80) REVERT: D 119 MET cc_start: 0.8483 (tpp) cc_final: 0.8215 (tmm) REVERT: D 503 MET cc_start: 0.6900 (tpp) cc_final: 0.5959 (tpp) REVERT: D 601 MET cc_start: 0.7726 (tmm) cc_final: 0.7116 (tmm) REVERT: D 622 MET cc_start: 0.8896 (tpt) cc_final: 0.8637 (mmm) REVERT: D 704 CYS cc_start: 0.7957 (p) cc_final: 0.7092 (p) REVERT: D 715 ASP cc_start: 0.6399 (t0) cc_final: 0.5416 (t0) REVERT: D 760 PHE cc_start: 0.7064 (m-80) cc_final: 0.6563 (m-80) outliers start: 48 outliers final: 40 residues processed: 296 average time/residue: 0.2933 time to fit residues: 139.7727 Evaluate side-chains 300 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 0.0870 chunk 254 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21220 Z= 0.243 Angle : 0.611 10.032 28712 Z= 0.312 Chirality : 0.043 0.167 3388 Planarity : 0.004 0.045 3720 Dihedral : 4.188 17.544 2932 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 2.54 % Allowed : 21.75 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2728 helix: 0.53 (0.16), residues: 1220 sheet: -1.84 (0.24), residues: 432 loop : -2.16 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 748 HIS 0.004 0.001 HIS C 607 PHE 0.009 0.001 PHE D 335 TYR 0.019 0.001 TYR C 631 ARG 0.005 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8458 (tpp) cc_final: 0.8195 (tmm) REVERT: A 503 MET cc_start: 0.6895 (tpp) cc_final: 0.5960 (tpp) REVERT: A 601 MET cc_start: 0.7808 (tmm) cc_final: 0.7026 (tmm) REVERT: A 622 MET cc_start: 0.8873 (tpt) cc_final: 0.8616 (mmm) REVERT: A 704 CYS cc_start: 0.8000 (p) cc_final: 0.7131 (p) REVERT: A 715 ASP cc_start: 0.6401 (t0) cc_final: 0.5401 (t0) REVERT: A 760 PHE cc_start: 0.7114 (m-80) cc_final: 0.6610 (m-80) REVERT: B 119 MET cc_start: 0.8458 (tpp) cc_final: 0.8194 (tmm) REVERT: B 503 MET cc_start: 0.6894 (tpp) cc_final: 0.5959 (tpp) REVERT: B 601 MET cc_start: 0.7808 (tmm) cc_final: 0.7028 (tmm) REVERT: B 622 MET cc_start: 0.8873 (tpt) cc_final: 0.8616 (mmm) REVERT: B 704 CYS cc_start: 0.8003 (p) cc_final: 0.7133 (p) REVERT: B 715 ASP cc_start: 0.6400 (t0) cc_final: 0.5404 (t0) REVERT: B 760 PHE cc_start: 0.7112 (m-80) cc_final: 0.6609 (m-80) REVERT: C 119 MET cc_start: 0.8460 (tpp) cc_final: 0.8197 (tmm) REVERT: C 503 MET cc_start: 0.6897 (tpp) cc_final: 0.5964 (tpp) REVERT: C 601 MET cc_start: 0.7808 (tmm) cc_final: 0.7026 (tmm) REVERT: C 622 MET cc_start: 0.8873 (tpt) cc_final: 0.8616 (mmm) REVERT: C 704 CYS cc_start: 0.8003 (p) cc_final: 0.7126 (p) REVERT: C 715 ASP cc_start: 0.6398 (t0) cc_final: 0.5401 (t0) REVERT: C 760 PHE cc_start: 0.7109 (m-80) cc_final: 0.6607 (m-80) REVERT: D 119 MET cc_start: 0.8459 (tpp) cc_final: 0.8193 (tmm) REVERT: D 503 MET cc_start: 0.6897 (tpp) cc_final: 0.5961 (tpp) REVERT: D 601 MET cc_start: 0.7813 (tmm) cc_final: 0.7029 (tmm) REVERT: D 622 MET cc_start: 0.8873 (tpt) cc_final: 0.8617 (mmm) REVERT: D 704 CYS cc_start: 0.7997 (p) cc_final: 0.7125 (p) REVERT: D 715 ASP cc_start: 0.6399 (t0) cc_final: 0.5401 (t0) REVERT: D 760 PHE cc_start: 0.7115 (m-80) cc_final: 0.6612 (m-80) outliers start: 57 outliers final: 44 residues processed: 309 average time/residue: 0.2898 time to fit residues: 144.9966 Evaluate side-chains 306 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 485 ASN Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 485 ASN Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 274 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21220 Z= 0.321 Angle : 0.653 9.314 28712 Z= 0.332 Chirality : 0.045 0.183 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.476 22.863 2932 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.45 % Allowed : 22.33 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2728 helix: 0.45 (0.16), residues: 1212 sheet: -1.83 (0.24), residues: 432 loop : -2.25 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 748 HIS 0.004 0.001 HIS A 707 PHE 0.012 0.001 PHE B 335 TYR 0.015 0.001 TYR C 631 ARG 0.002 0.000 ARG C 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 258 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8492 (tpp) cc_final: 0.8141 (tmm) REVERT: A 503 MET cc_start: 0.6901 (tpp) cc_final: 0.5878 (mpp) REVERT: A 601 MET cc_start: 0.7838 (tmm) cc_final: 0.6997 (tmm) REVERT: A 622 MET cc_start: 0.8857 (tpt) cc_final: 0.8574 (mmm) REVERT: A 704 CYS cc_start: 0.8072 (p) cc_final: 0.7207 (p) REVERT: A 715 ASP cc_start: 0.6385 (t0) cc_final: 0.5300 (t0) REVERT: A 760 PHE cc_start: 0.7149 (m-80) cc_final: 0.6628 (m-80) REVERT: B 119 MET cc_start: 0.8462 (tpp) cc_final: 0.8108 (tmm) REVERT: B 503 MET cc_start: 0.6900 (tpp) cc_final: 0.5875 (mpp) REVERT: B 601 MET cc_start: 0.7839 (tmm) cc_final: 0.6996 (tmm) REVERT: B 622 MET cc_start: 0.8856 (tpt) cc_final: 0.8574 (mmm) REVERT: B 704 CYS cc_start: 0.8079 (p) cc_final: 0.7213 (p) REVERT: B 715 ASP cc_start: 0.6386 (t0) cc_final: 0.5302 (t0) REVERT: B 760 PHE cc_start: 0.7149 (m-80) cc_final: 0.6628 (m-80) REVERT: C 119 MET cc_start: 0.8460 (tpp) cc_final: 0.8110 (tmm) REVERT: C 503 MET cc_start: 0.6898 (tpp) cc_final: 0.5836 (mpp) REVERT: C 601 MET cc_start: 0.7836 (tmm) cc_final: 0.6996 (tmm) REVERT: C 622 MET cc_start: 0.8856 (tpt) cc_final: 0.8575 (mmm) REVERT: C 704 CYS cc_start: 0.8069 (p) cc_final: 0.7201 (p) REVERT: C 715 ASP cc_start: 0.6385 (t0) cc_final: 0.5302 (t0) REVERT: C 760 PHE cc_start: 0.7147 (m-80) cc_final: 0.6626 (m-80) REVERT: D 119 MET cc_start: 0.8462 (tpp) cc_final: 0.8108 (tmm) REVERT: D 503 MET cc_start: 0.6901 (tpp) cc_final: 0.5839 (mpp) REVERT: D 601 MET cc_start: 0.7841 (tmm) cc_final: 0.6998 (tmm) REVERT: D 622 MET cc_start: 0.8858 (tpt) cc_final: 0.8576 (mmm) REVERT: D 704 CYS cc_start: 0.8068 (p) cc_final: 0.7205 (p) REVERT: D 715 ASP cc_start: 0.6386 (t0) cc_final: 0.5301 (t0) REVERT: D 760 PHE cc_start: 0.7152 (m-80) cc_final: 0.6629 (m-80) outliers start: 55 outliers final: 44 residues processed: 293 average time/residue: 0.2914 time to fit residues: 137.7827 Evaluate side-chains 290 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 485 ASN Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 485 ASN Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.155271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099988 restraints weight = 38768.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104760 restraints weight = 19103.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107354 restraints weight = 11420.252| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21220 Z= 0.214 Angle : 0.610 9.263 28712 Z= 0.309 Chirality : 0.044 0.146 3388 Planarity : 0.004 0.044 3720 Dihedral : 4.246 21.946 2932 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.28 % Favored : 94.57 % Rotamer: Outliers : 2.41 % Allowed : 22.46 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.17), residues: 2728 helix: 0.60 (0.16), residues: 1212 sheet: -1.64 (0.25), residues: 432 loop : -2.16 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 748 HIS 0.004 0.001 HIS D 92 PHE 0.009 0.001 PHE D 335 TYR 0.007 0.001 TYR A 631 ARG 0.006 0.000 ARG D 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.80 seconds wall clock time: 67 minutes 56.94 seconds (4076.94 seconds total)