Starting phenix.real_space_refine on Fri Feb 16 19:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2024/7bx8_30236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2024/7bx8_30236.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/7bx8_30236/02_2024/7bx8_30236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2024/7bx8_30236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2024/7bx8_30236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2024/7bx8_30236.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= 0.008 sd= 0.083 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 68 5.16 5 C 10508 2.51 5 N 2818 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "A TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A ASP 926": "OD1" <-> "OD2" Residue "A ASP 943": "OD1" <-> "OD2" Residue "A PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1029": "NH1" <-> "NH2" Residue "A PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 526": "NH1" <-> "NH2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B GLU 679": "OE1" <-> "OE2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 772": "OD1" <-> "OD2" Residue "B ARG 777": "NH1" <-> "NH2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 851": "OE1" <-> "OE2" Residue "B ARG 901": "NH1" <-> "NH2" Residue "B ASP 926": "OD1" <-> "OD2" Residue "B ASP 943": "OD1" <-> "OD2" Residue "B PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1029": "NH1" <-> "NH2" Residue "B PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7655 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 75, 'TRANS': 962} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 188 Chain: "C" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 497 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 7655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7655 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 75, 'TRANS': 962} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 188 Chain: "D" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 497 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 9.02, per 1000 atoms: 0.55 Number of scatterers: 16304 At special positions: 0 Unit cell: (127.1, 124.64, 139.4, 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 68 16.00 O 2910 8.00 N 2818 7.00 C 10508 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: 7.83 Conformation dependent library (CDL) restraints added in 3.2 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 43.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 26 through 43 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 219 through 245 Processing helix chain 'A' and resid 263 through 280 removed outlier: 4.094A pdb=" N MET A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 3.792A pdb=" N MET A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.884A pdb=" N ARG A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.642A pdb=" N ALA A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.868A pdb=" N MET A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 390 through 412 removed outlier: 3.778A pdb=" N ILE A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.606A pdb=" N THR A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.246A pdb=" N VAL A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.886A pdb=" N ILE A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.620A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 499 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.535A pdb=" N THR A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.798A pdb=" N ILE A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 586 Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.500A pdb=" N ALA A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 627 removed outlier: 3.523A pdb=" N ARG A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 676 removed outlier: 3.530A pdb=" N LEU A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.793A pdb=" N ASP A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 713 removed outlier: 3.921A pdb=" N VAL A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.568A pdb=" N TRP A 796 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 958 through 962 Processing helix chain 'A' and resid 1001 through 1008 Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.562A pdb=" N TRP A1012 " --> pdb=" O SER A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1018 removed outlier: 3.610A pdb=" N GLY A1018 " --> pdb=" O GLY A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 removed outlier: 3.574A pdb=" N ASP A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A1026 " --> pdb=" O GLY A1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.887A pdb=" N ILE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.786A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.007A pdb=" N VAL C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 219 through 245 Processing helix chain 'B' and resid 263 through 280 removed outlier: 4.093A pdb=" N MET B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 300 removed outlier: 3.793A pdb=" N MET B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.883A pdb=" N ARG B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 354 removed outlier: 3.641A pdb=" N ALA B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 366 through 385 removed outlier: 3.867A pdb=" N MET B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Proline residue: B 383 - end of helix Processing helix chain 'B' and resid 390 through 412 removed outlier: 3.777A pdb=" N ILE B 394 " --> pdb=" O PRO B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.606A pdb=" N THR B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 4.246A pdb=" N VAL B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.886A pdb=" N ILE B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.620A pdb=" N VAL B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 499 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.535A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 546 Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.798A pdb=" N ILE B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 569 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 586 Processing helix chain 'B' and resid 587 through 600 removed outlier: 3.500A pdb=" N ALA B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 627 removed outlier: 3.524A pdb=" N ARG B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 676 removed outlier: 3.530A pdb=" N LEU B 672 " --> pdb=" O TRP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.792A pdb=" N ASP B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 713 removed outlier: 3.922A pdb=" N VAL B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 726 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.568A pdb=" N TRP B 796 " --> pdb=" O ASP B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 958 through 962 Processing helix chain 'B' and resid 1001 through 1008 Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 3.561A pdb=" N TRP B1012 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1018 removed outlier: 3.609A pdb=" N GLY B1018 " --> pdb=" O GLY B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1028 removed outlier: 3.574A pdb=" N ASP B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B1026 " --> pdb=" O GLY B1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 20 Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.887A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 67 removed outlier: 3.786A pdb=" N ALA D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 4.007A pdb=" N VAL D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.615A pdb=" N HIS A 217 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 49 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A1070 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 4.152A pdb=" N PHE A 99 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 116 " --> pdb=" O PHE A 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 956 through 957 Processing sheet with id=AA7, first strand: chain 'A' and resid 749 through 750 removed outlier: 4.268A pdb=" N THR A 749 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 930 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 929 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA9, first strand: chain 'A' and resid 859 through 862 Processing sheet with id=AB1, first strand: chain 'A' and resid 870 through 871 removed outlier: 3.507A pdb=" N GLY A 870 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 878 " --> pdb=" O GLY A 870 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 986 through 987 Processing sheet with id=AB3, first strand: chain 'A' and resid 996 through 999 Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 218 removed outlier: 3.615A pdb=" N HIS B 217 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 49 " --> pdb=" O SER B1070 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B1070 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AB6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB7, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100 removed outlier: 4.152A pdb=" N PHE B 99 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 116 " --> pdb=" O PHE B 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AC1, first strand: chain 'B' and resid 749 through 750 removed outlier: 4.267A pdb=" N THR B 749 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 930 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 929 " --> pdb=" O ALA B 888 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 889 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AC3, first strand: chain 'B' and resid 859 through 862 Processing sheet with id=AC4, first strand: chain 'B' and resid 870 through 871 removed outlier: 3.506A pdb=" N GLY B 870 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 878 " --> pdb=" O GLY B 870 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 986 through 987 Processing sheet with id=AC6, first strand: chain 'B' and resid 996 through 999 660 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 8.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2623 1.32 - 1.44: 4387 1.44 - 1.56: 9558 1.56 - 1.69: 2 1.69 - 1.81: 120 Bond restraints: 16690 Sorted by residual: bond pdb=" N ASN B 637 " pdb=" CA ASN B 637 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.29e-02 6.01e+03 1.51e+01 bond pdb=" N ASN A 637 " pdb=" CA ASN A 637 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.29e-02 6.01e+03 1.50e+01 bond pdb=" C ASN A 637 " pdb=" O ASN A 637 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.26e-02 6.30e+03 1.11e+01 bond pdb=" C ASN B 637 " pdb=" O ASN B 637 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" N LYS A 577 " pdb=" CA LYS A 577 " ideal model delta sigma weight residual 1.461 1.431 0.030 1.20e-02 6.94e+03 6.25e+00 ... (remaining 16685 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.98: 550 104.98 - 112.79: 8735 112.79 - 120.61: 7602 120.61 - 128.43: 5845 128.43 - 136.24: 178 Bond angle restraints: 22910 Sorted by residual: angle pdb=" N PRO B 315 " pdb=" CA PRO B 315 " pdb=" C PRO B 315 " ideal model delta sigma weight residual 113.40 103.57 9.83 1.34e+00 5.57e-01 5.38e+01 angle pdb=" N PRO A 315 " pdb=" CA PRO A 315 " pdb=" C PRO A 315 " ideal model delta sigma weight residual 113.40 103.58 9.82 1.34e+00 5.57e-01 5.37e+01 angle pdb=" N GLY D 21 " pdb=" CA GLY D 21 " pdb=" C GLY D 21 " ideal model delta sigma weight residual 113.48 124.11 -10.63 1.46e+00 4.69e-01 5.31e+01 angle pdb=" N GLY C 21 " pdb=" CA GLY C 21 " pdb=" C GLY C 21 " ideal model delta sigma weight residual 113.48 124.10 -10.62 1.46e+00 4.69e-01 5.29e+01 angle pdb=" N PHE D 33 " pdb=" CA PHE D 33 " pdb=" C PHE D 33 " ideal model delta sigma weight residual 111.11 119.72 -8.61 1.20e+00 6.94e-01 5.14e+01 ... (remaining 22905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 8855 16.94 - 33.89: 737 33.89 - 50.83: 156 50.83 - 67.77: 40 67.77 - 84.72: 10 Dihedral angle restraints: 9798 sinusoidal: 3436 harmonic: 6362 Sorted by residual: dihedral pdb=" CA VAL B 98 " pdb=" C VAL B 98 " pdb=" N PHE B 99 " pdb=" CA PHE B 99 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL A 98 " pdb=" C VAL A 98 " pdb=" N PHE A 99 " pdb=" CA PHE A 99 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LEU B 859 " pdb=" C LEU B 859 " pdb=" N VAL B 860 " pdb=" CA VAL B 860 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 9795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2146 0.084 - 0.169: 486 0.169 - 0.253: 94 0.253 - 0.338: 18 0.338 - 0.422: 10 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CA PHE D 33 " pdb=" N PHE D 33 " pdb=" C PHE D 33 " pdb=" CB PHE D 33 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA PHE C 33 " pdb=" N PHE C 33 " pdb=" C PHE C 33 " pdb=" CB PHE C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR B 910 " pdb=" CA THR B 910 " pdb=" OG1 THR B 910 " pdb=" CG2 THR B 910 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 2751 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 313 " -0.028 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C GLU B 313 " 0.101 2.00e-02 2.50e+03 pdb=" O GLU B 313 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP B 314 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 313 " -0.028 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" C GLU A 313 " 0.101 2.00e-02 2.50e+03 pdb=" O GLU A 313 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP A 314 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 823 " 0.083 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO A 824 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 824 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 824 " 0.063 5.00e-02 4.00e+02 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4811 2.82 - 3.34: 15751 3.34 - 3.86: 26914 3.86 - 4.38: 29559 4.38 - 4.90: 51167 Nonbonded interactions: 128202 Sorted by model distance: nonbonded pdb=" OG1 THR A 157 " pdb=" O TYR A 180 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR B 157 " pdb=" O TYR B 180 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR A 867 " pdb=" OD1 ASP A 943 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR B 867 " pdb=" OD1 ASP B 943 " model vdw 2.300 2.440 nonbonded pdb=" O LEU B 802 " pdb=" OG1 THR B 811 " model vdw 2.312 2.440 ... (remaining 128197 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' } ncs_group { reference = 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: 0.410 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: 0.000 Extract box with map and model: 4.540 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 48.050 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 16690 Z= 0.536 Angle : 1.308 12.933 22910 Z= 0.763 Chirality : 0.078 0.422 2754 Planarity : 0.011 0.122 2922 Dihedral : 13.917 84.718 5714 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.55 % Favored : 88.36 % Rotamer: Outliers : 1.37 % Allowed : 11.30 % Favored : 87.33 % 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: -4.54 (0.14), residues: 2216 helix: -2.64 (0.12), residues: 846 sheet: -3.12 (0.30), residues: 218 loop : -3.33 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B1041 HIS 0.014 0.002 HIS B1069 PHE 0.034 0.003 PHE B 99 TYR 0.037 0.002 TYR D 76 ARG 0.006 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 375 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 255 ILE cc_start: 0.9101 (mp) cc_final: 0.8776 (mp) REVERT: A 386 ASN cc_start: 0.8695 (t0) cc_final: 0.8327 (t0) REVERT: A 554 ARG cc_start: 0.7272 (tmm-80) cc_final: 0.6772 (ttt90) REVERT: A 565 PHE cc_start: 0.8650 (m-80) cc_final: 0.8425 (m-80) REVERT: A 592 MET cc_start: 0.9124 (tpp) cc_final: 0.8825 (tpp) REVERT: A 624 PHE cc_start: 0.8499 (t80) cc_final: 0.8219 (t80) REVERT: A 698 MET cc_start: 0.8521 (mmm) cc_final: 0.8286 (mmm) REVERT: A 914 ARG cc_start: 0.8389 (ptp90) cc_final: 0.7978 (ptt-90) REVERT: A 1006 LEU cc_start: 0.9067 (tp) cc_final: 0.8865 (tt) REVERT: B 28 TRP cc_start: 0.7951 (t-100) cc_final: 0.7746 (m-10) REVERT: B 114 MET cc_start: 0.8950 (ttp) cc_final: 0.8676 (ttp) REVERT: B 255 ILE cc_start: 0.9047 (mp) cc_final: 0.8770 (mp) REVERT: B 289 ILE cc_start: 0.9226 (mm) cc_final: 0.9021 (mt) REVERT: B 370 MET cc_start: 0.8052 (ttm) cc_final: 0.7748 (ttm) REVERT: B 386 ASN cc_start: 0.8676 (t0) cc_final: 0.8254 (t0) REVERT: B 554 ARG cc_start: 0.7271 (tmm-80) cc_final: 0.6715 (ttt90) REVERT: B 561 MET cc_start: 0.8263 (mmt) cc_final: 0.7823 (mmt) REVERT: B 592 MET cc_start: 0.9122 (tpp) cc_final: 0.8548 (tpp) REVERT: B 624 PHE cc_start: 0.8550 (t80) cc_final: 0.7927 (t80) REVERT: B 698 MET cc_start: 0.8536 (mmm) cc_final: 0.7823 (mtp) REVERT: B 1003 TYR cc_start: 0.8580 (m-80) cc_final: 0.8355 (m-80) REVERT: B 1006 LEU cc_start: 0.9105 (tp) cc_final: 0.8895 (tt) REVERT: B 1010 ASP cc_start: 0.7380 (m-30) cc_final: 0.7094 (m-30) outliers start: 22 outliers final: 5 residues processed: 387 average time/residue: 0.2620 time to fit residues: 153.0574 Evaluate side-chains 275 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 270 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 993 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 57 ASN A 60 GLN A 112 ASN A 321 ASN A 386 ASN A 431 GLN A1013 GLN B 51 GLN B 57 ASN B 60 GLN B 112 ASN B 321 ASN B 386 ASN B 431 GLN B1013 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16690 Z= 0.225 Angle : 0.692 12.821 22910 Z= 0.347 Chirality : 0.045 0.210 2754 Planarity : 0.006 0.073 2922 Dihedral : 5.665 46.531 2407 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.10 % Allowed : 18.39 % Favored : 77.52 % 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: -2.72 (0.16), residues: 2216 helix: -0.54 (0.16), residues: 866 sheet: -2.32 (0.35), residues: 198 loop : -2.81 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 944 HIS 0.005 0.001 HIS A 252 PHE 0.035 0.002 PHE A 99 TYR 0.013 0.001 TYR D 55 ARG 0.016 0.001 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 282 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8404 (pp) REVERT: A 554 ARG cc_start: 0.7076 (tmm-80) cc_final: 0.6794 (ttt90) REVERT: A 561 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: A 565 PHE cc_start: 0.8602 (m-80) cc_final: 0.8359 (m-80) REVERT: A 624 PHE cc_start: 0.8564 (t80) cc_final: 0.8286 (t80) REVERT: A 635 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8132 (m) REVERT: A 698 MET cc_start: 0.8349 (mmm) cc_final: 0.8088 (mmm) REVERT: A 884 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7134 (p0) REVERT: A 1006 LEU cc_start: 0.9067 (tp) cc_final: 0.8853 (tt) REVERT: B 46 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 114 MET cc_start: 0.8865 (ttp) cc_final: 0.8567 (ttp) REVERT: B 301 TYR cc_start: 0.8294 (p90) cc_final: 0.7859 (p90) REVERT: B 370 MET cc_start: 0.8075 (ttm) cc_final: 0.7719 (ttm) REVERT: B 386 ASN cc_start: 0.8408 (t0) cc_final: 0.7700 (t0) REVERT: B 554 ARG cc_start: 0.7038 (tmm-80) cc_final: 0.6726 (ttt90) REVERT: B 592 MET cc_start: 0.9176 (tpp) cc_final: 0.8908 (tpt) REVERT: B 612 MET cc_start: 0.9184 (mmm) cc_final: 0.8705 (mmm) REVERT: B 635 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8160 (m) REVERT: B 731 CYS cc_start: 0.7006 (m) cc_final: 0.6796 (m) REVERT: B 1006 LEU cc_start: 0.9046 (tp) cc_final: 0.8828 (tt) REVERT: B 1047 SER cc_start: 0.8491 (p) cc_final: 0.8104 (m) outliers start: 66 outliers final: 38 residues processed: 326 average time/residue: 0.2628 time to fit residues: 133.3103 Evaluate side-chains 282 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 0.0050 chunk 216 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 548 HIS B1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16690 Z= 0.202 Angle : 0.636 12.062 22910 Z= 0.314 Chirality : 0.044 0.200 2754 Planarity : 0.005 0.049 2922 Dihedral : 5.191 45.485 2406 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.91 % Allowed : 19.44 % Favored : 75.65 % 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: -2.00 (0.17), residues: 2216 helix: 0.27 (0.17), residues: 878 sheet: -2.07 (0.34), residues: 214 loop : -2.58 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1041 HIS 0.003 0.001 HIS B 581 PHE 0.024 0.001 PHE B 99 TYR 0.022 0.001 TYR A 301 ARG 0.005 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 375 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8889 (mm) REVERT: A 525 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6986 (tmm160) REVERT: A 554 ARG cc_start: 0.7013 (tmm-80) cc_final: 0.6808 (ttp80) REVERT: A 565 PHE cc_start: 0.8557 (m-80) cc_final: 0.8349 (m-80) REVERT: A 624 PHE cc_start: 0.8545 (t80) cc_final: 0.8264 (t80) REVERT: A 635 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8027 (m) REVERT: A 659 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 698 MET cc_start: 0.8351 (mmm) cc_final: 0.7960 (mmm) REVERT: A 1014 ASP cc_start: 0.7849 (t0) cc_final: 0.7643 (t0) REVERT: B 46 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8376 (pp) REVERT: B 114 MET cc_start: 0.8783 (ttp) cc_final: 0.8565 (ttp) REVERT: B 273 MET cc_start: 0.8772 (tpp) cc_final: 0.8307 (tpt) REVERT: B 301 TYR cc_start: 0.8298 (p90) cc_final: 0.7821 (p90) REVERT: B 370 MET cc_start: 0.8079 (ttm) cc_final: 0.7737 (ttm) REVERT: B 382 MET cc_start: 0.8589 (mtp) cc_final: 0.8346 (mtp) REVERT: B 386 ASN cc_start: 0.8291 (t0) cc_final: 0.7694 (t0) REVERT: B 543 MET cc_start: 0.8350 (mmm) cc_final: 0.8044 (mmm) REVERT: B 554 ARG cc_start: 0.7128 (tmm-80) cc_final: 0.6755 (ttt90) REVERT: B 612 MET cc_start: 0.9201 (mmm) cc_final: 0.8825 (mmm) REVERT: B 1006 LEU cc_start: 0.9034 (tp) cc_final: 0.8798 (tt) outliers start: 79 outliers final: 37 residues processed: 319 average time/residue: 0.2393 time to fit residues: 120.6023 Evaluate side-chains 297 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 190 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS B 393 GLN B 548 HIS B1013 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16690 Z= 0.183 Angle : 0.611 11.664 22910 Z= 0.300 Chirality : 0.043 0.222 2754 Planarity : 0.004 0.043 2922 Dihedral : 4.954 43.456 2406 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.71 % Allowed : 20.00 % Favored : 73.29 % 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: -1.56 (0.18), residues: 2216 helix: 0.67 (0.17), residues: 882 sheet: -1.97 (0.34), residues: 214 loop : -2.35 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 58 HIS 0.003 0.001 HIS B 217 PHE 0.021 0.001 PHE B 99 TYR 0.022 0.001 TYR A 301 ARG 0.004 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 271 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (mm) REVERT: A 393 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8205 (mp10) REVERT: A 489 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 525 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6907 (tmm160) REVERT: A 554 ARG cc_start: 0.7056 (tmm-80) cc_final: 0.6672 (ttt90) REVERT: A 561 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.6779 (mpp) REVERT: A 565 PHE cc_start: 0.8411 (m-80) cc_final: 0.7917 (m-80) REVERT: A 624 PHE cc_start: 0.8570 (t80) cc_final: 0.8288 (t80) REVERT: A 635 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 659 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7965 (t80) REVERT: A 698 MET cc_start: 0.8232 (mmm) cc_final: 0.8019 (mmm) REVERT: A 758 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.3596 (pp) REVERT: A 1014 ASP cc_start: 0.7811 (t0) cc_final: 0.7299 (t0) REVERT: A 1016 ILE cc_start: 0.9178 (tp) cc_final: 0.8771 (tp) REVERT: B 46 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 273 MET cc_start: 0.8817 (tpp) cc_final: 0.8304 (tpt) REVERT: B 382 MET cc_start: 0.8562 (mtp) cc_final: 0.8352 (mtp) REVERT: B 386 ASN cc_start: 0.8299 (t0) cc_final: 0.7739 (t0) REVERT: B 543 MET cc_start: 0.8328 (mmm) cc_final: 0.7913 (mmm) REVERT: B 554 ARG cc_start: 0.7125 (tmm-80) cc_final: 0.6729 (ttt90) REVERT: B 612 MET cc_start: 0.9221 (mmm) cc_final: 0.8875 (mmm) REVERT: B 736 ASP cc_start: 0.8206 (p0) cc_final: 0.7977 (p0) REVERT: B 985 LEU cc_start: 0.9132 (pt) cc_final: 0.8532 (mp) outliers start: 108 outliers final: 61 residues processed: 342 average time/residue: 0.2409 time to fit residues: 129.4040 Evaluate side-chains 322 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 253 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 548 HIS A 610 ASN A1013 GLN B 393 GLN B 548 HIS B 610 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16690 Z= 0.453 Angle : 0.755 10.349 22910 Z= 0.378 Chirality : 0.047 0.206 2754 Planarity : 0.005 0.047 2922 Dihedral : 5.302 41.990 2406 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 7.08 % Allowed : 21.80 % Favored : 71.12 % 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: -1.75 (0.18), residues: 2216 helix: 0.48 (0.17), residues: 884 sheet: -1.97 (0.32), residues: 236 loop : -2.44 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 58 HIS 0.006 0.001 HIS B 581 PHE 0.027 0.002 PHE B 99 TYR 0.023 0.002 TYR A 301 ARG 0.003 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 261 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 449 LEU cc_start: 0.8746 (tt) cc_final: 0.8523 (tt) REVERT: A 465 ILE cc_start: 0.8700 (tp) cc_final: 0.8442 (tp) REVERT: A 489 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8815 (mm) REVERT: A 554 ARG cc_start: 0.7572 (tmm-80) cc_final: 0.7139 (ttt90) REVERT: A 561 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: A 624 PHE cc_start: 0.8687 (t80) cc_final: 0.8361 (t80) REVERT: A 659 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 758 LEU cc_start: 0.4343 (OUTLIER) cc_final: 0.3562 (pp) REVERT: A 1014 ASP cc_start: 0.8059 (t0) cc_final: 0.7484 (t0) REVERT: A 1016 ILE cc_start: 0.9203 (tp) cc_final: 0.8750 (tp) REVERT: B 382 MET cc_start: 0.8754 (mtp) cc_final: 0.8534 (mtp) REVERT: B 465 ILE cc_start: 0.8686 (tp) cc_final: 0.8302 (tp) REVERT: B 554 ARG cc_start: 0.7555 (tmm-80) cc_final: 0.7044 (ttt90) REVERT: B 612 MET cc_start: 0.9215 (mmm) cc_final: 0.8888 (mmm) REVERT: B 736 ASP cc_start: 0.8291 (p0) cc_final: 0.7904 (p0) REVERT: B 758 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3640 (pp) REVERT: B 985 LEU cc_start: 0.9153 (pt) cc_final: 0.8524 (mp) REVERT: B 1041 TRP cc_start: 0.8233 (m-90) cc_final: 0.7970 (m-90) outliers start: 114 outliers final: 83 residues processed: 333 average time/residue: 0.2268 time to fit residues: 121.3726 Evaluate side-chains 337 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 248 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 884 ASP Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.0670 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 40.0000 chunk 52 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 548 HIS A1013 GLN B 393 GLN B 548 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16690 Z= 0.175 Angle : 0.622 10.890 22910 Z= 0.302 Chirality : 0.043 0.187 2754 Planarity : 0.004 0.041 2922 Dihedral : 4.961 36.432 2406 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.53 % Allowed : 23.42 % Favored : 71.06 % 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: -1.34 (0.18), residues: 2216 helix: 0.94 (0.18), residues: 876 sheet: -1.83 (0.33), residues: 222 loop : -2.30 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 944 HIS 0.005 0.001 HIS A 298 PHE 0.024 0.001 PHE B 99 TYR 0.012 0.001 TYR B 305 ARG 0.003 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 276 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 489 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8730 (mm) REVERT: A 554 ARG cc_start: 0.7202 (tmm-80) cc_final: 0.6848 (ttt90) REVERT: A 561 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7662 (mpp) REVERT: A 624 PHE cc_start: 0.8570 (t80) cc_final: 0.8259 (t80) REVERT: A 635 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8023 (m) REVERT: A 659 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (t80) REVERT: A 758 LEU cc_start: 0.4399 (OUTLIER) cc_final: 0.3623 (pp) REVERT: A 1014 ASP cc_start: 0.7857 (t0) cc_final: 0.7485 (t0) REVERT: A 1016 ILE cc_start: 0.9120 (tp) cc_final: 0.8781 (tp) REVERT: B 273 MET cc_start: 0.8658 (tpt) cc_final: 0.8224 (tpt) REVERT: B 382 MET cc_start: 0.8589 (mtp) cc_final: 0.8266 (mtp) REVERT: B 386 ASN cc_start: 0.8373 (t0) cc_final: 0.7771 (t0) REVERT: B 554 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6781 (ttt90) REVERT: B 612 MET cc_start: 0.9170 (mmm) cc_final: 0.8819 (mmm) REVERT: B 736 ASP cc_start: 0.8197 (p0) cc_final: 0.7865 (p0) REVERT: B 758 LEU cc_start: 0.3812 (OUTLIER) cc_final: 0.3328 (pp) REVERT: B 985 LEU cc_start: 0.9008 (pt) cc_final: 0.8546 (mp) REVERT: B 1047 SER cc_start: 0.8495 (p) cc_final: 0.8088 (m) outliers start: 89 outliers final: 58 residues processed: 337 average time/residue: 0.2395 time to fit residues: 128.1473 Evaluate side-chains 322 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 257 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 118 optimal weight: 0.0770 chunk 212 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 97 optimal weight: 0.0070 overall best weight: 3.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN A 548 HIS ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16690 Z= 0.270 Angle : 0.650 9.452 22910 Z= 0.318 Chirality : 0.044 0.190 2754 Planarity : 0.004 0.042 2922 Dihedral : 4.924 36.072 2406 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 6.52 % Allowed : 24.16 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.32 (0.18), residues: 2216 helix: 0.90 (0.17), residues: 884 sheet: -1.80 (0.31), residues: 238 loop : -2.25 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 944 HIS 0.005 0.001 HIS A 581 PHE 0.024 0.001 PHE B 99 TYR 0.019 0.001 TYR A 301 ARG 0.005 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 257 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 489 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8762 (mm) REVERT: A 554 ARG cc_start: 0.7346 (tmm-80) cc_final: 0.6974 (ttt90) REVERT: A 561 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7480 (mpp) REVERT: A 624 PHE cc_start: 0.8646 (t80) cc_final: 0.8318 (t80) REVERT: A 635 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8064 (m) REVERT: A 659 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8064 (t80) REVERT: A 758 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.3655 (pp) REVERT: A 1014 ASP cc_start: 0.7903 (t0) cc_final: 0.7574 (t0) REVERT: A 1016 ILE cc_start: 0.9159 (tp) cc_final: 0.8843 (tp) REVERT: B 273 MET cc_start: 0.8724 (tpt) cc_final: 0.8136 (tpt) REVERT: B 382 MET cc_start: 0.8627 (mtp) cc_final: 0.7885 (mtp) REVERT: B 386 ASN cc_start: 0.8428 (t0) cc_final: 0.7854 (t0) REVERT: B 554 ARG cc_start: 0.7364 (tmm-80) cc_final: 0.6980 (ttt90) REVERT: B 612 MET cc_start: 0.9216 (mmm) cc_final: 0.8887 (mmm) REVERT: B 703 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6978 (mpp) REVERT: B 736 ASP cc_start: 0.8279 (p0) cc_final: 0.7941 (p0) REVERT: B 758 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3488 (pp) REVERT: B 985 LEU cc_start: 0.9185 (pt) cc_final: 0.8600 (mp) outliers start: 105 outliers final: 77 residues processed: 328 average time/residue: 0.2234 time to fit residues: 117.7094 Evaluate side-chains 335 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 250 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16690 Z= 0.379 Angle : 0.707 8.735 22910 Z= 0.351 Chirality : 0.046 0.169 2754 Planarity : 0.005 0.044 2922 Dihedral : 5.123 39.672 2406 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 6.46 % Allowed : 24.22 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2216 helix: 0.81 (0.17), residues: 884 sheet: -1.89 (0.30), residues: 238 loop : -2.33 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 944 HIS 0.005 0.001 HIS A 581 PHE 0.025 0.002 PHE B 99 TYR 0.021 0.002 TYR A 301 ARG 0.003 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 253 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8904 (mm) REVERT: A 489 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8806 (mm) REVERT: A 554 ARG cc_start: 0.7485 (tmm-80) cc_final: 0.7034 (ttt90) REVERT: A 561 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7357 (mpp) REVERT: A 572 MET cc_start: 0.6950 (tpt) cc_final: 0.6565 (tpp) REVERT: A 624 PHE cc_start: 0.8707 (t80) cc_final: 0.8359 (t80) REVERT: A 635 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8100 (m) REVERT: A 659 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8106 (t80) REVERT: A 758 LEU cc_start: 0.4462 (OUTLIER) cc_final: 0.3707 (pp) REVERT: A 1014 ASP cc_start: 0.7963 (t0) cc_final: 0.7608 (t0) REVERT: A 1016 ILE cc_start: 0.9170 (tp) cc_final: 0.8814 (tp) REVERT: B 554 ARG cc_start: 0.7466 (tmm-80) cc_final: 0.6962 (ttt90) REVERT: B 612 MET cc_start: 0.9196 (mmm) cc_final: 0.8874 (mmm) REVERT: B 736 ASP cc_start: 0.8262 (p0) cc_final: 0.7926 (p0) REVERT: B 758 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3572 (pp) REVERT: B 985 LEU cc_start: 0.9215 (pt) cc_final: 0.8604 (mp) outliers start: 104 outliers final: 83 residues processed: 322 average time/residue: 0.2466 time to fit residues: 125.4628 Evaluate side-chains 332 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 242 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1033 MET Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 884 ASP Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.0050 chunk 178 optimal weight: 8.9990 chunk 186 optimal weight: 0.0070 chunk 196 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN B1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16690 Z= 0.169 Angle : 0.630 10.819 22910 Z= 0.305 Chirality : 0.043 0.182 2754 Planarity : 0.004 0.042 2922 Dihedral : 4.830 35.672 2406 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.72 % Allowed : 26.46 % Favored : 68.82 % 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: -1.25 (0.18), residues: 2216 helix: 1.00 (0.18), residues: 888 sheet: -1.85 (0.30), residues: 242 loop : -2.24 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 944 HIS 0.003 0.001 HIS A 298 PHE 0.024 0.001 PHE B 99 TYR 0.013 0.001 TYR A 301 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 273 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8002 (t-100) cc_final: 0.7797 (t60) REVERT: A 375 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8859 (mm) REVERT: A 489 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 554 ARG cc_start: 0.7185 (tmm-80) cc_final: 0.6788 (ttt90) REVERT: A 561 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7290 (mpp) REVERT: A 572 MET cc_start: 0.6650 (tpt) cc_final: 0.6118 (tpp) REVERT: A 624 PHE cc_start: 0.8627 (t80) cc_final: 0.8265 (t80) REVERT: A 635 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 659 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8000 (t80) REVERT: A 698 MET cc_start: 0.8159 (tpp) cc_final: 0.7806 (mtp) REVERT: A 758 LEU cc_start: 0.4390 (OUTLIER) cc_final: 0.3519 (pp) REVERT: B 46 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8770 (pp) REVERT: B 273 MET cc_start: 0.8591 (tpt) cc_final: 0.8167 (tpt) REVERT: B 386 ASN cc_start: 0.8383 (t0) cc_final: 0.7799 (t0) REVERT: B 554 ARG cc_start: 0.7076 (tmm-80) cc_final: 0.6740 (ttt90) REVERT: B 572 MET cc_start: 0.6729 (tpt) cc_final: 0.6173 (tpp) REVERT: B 612 MET cc_start: 0.9210 (mmm) cc_final: 0.8865 (mmm) REVERT: B 698 MET cc_start: 0.8127 (tpp) cc_final: 0.7521 (mtp) REVERT: B 736 ASP cc_start: 0.8210 (p0) cc_final: 0.7934 (p0) REVERT: B 758 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.3271 (pp) REVERT: B 985 LEU cc_start: 0.9107 (pt) cc_final: 0.8605 (mp) REVERT: B 1017 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7913 (p0) REVERT: B 1047 SER cc_start: 0.8492 (p) cc_final: 0.8085 (m) outliers start: 76 outliers final: 59 residues processed: 326 average time/residue: 0.2395 time to fit residues: 124.0574 Evaluate side-chains 327 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 259 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 174 optimal weight: 0.0470 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16690 Z= 0.245 Angle : 0.664 11.717 22910 Z= 0.322 Chirality : 0.044 0.211 2754 Planarity : 0.004 0.041 2922 Dihedral : 4.823 36.574 2406 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.78 % Allowed : 26.65 % Favored : 68.57 % 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: -1.21 (0.18), residues: 2216 helix: 0.96 (0.18), residues: 890 sheet: -1.73 (0.30), residues: 238 loop : -2.18 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 944 HIS 0.004 0.001 HIS B 581 PHE 0.035 0.001 PHE A 193 TYR 0.018 0.001 TYR A 301 ARG 0.003 0.000 ARG B 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 256 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8040 (t-100) cc_final: 0.7828 (t60) REVERT: A 375 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 489 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 554 ARG cc_start: 0.7366 (tmm-80) cc_final: 0.6968 (ttt90) REVERT: A 561 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7582 (mpp) REVERT: A 572 MET cc_start: 0.6744 (tpt) cc_final: 0.6129 (tpp) REVERT: A 624 PHE cc_start: 0.8687 (t80) cc_final: 0.8302 (t80) REVERT: A 635 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 659 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8033 (t80) REVERT: A 698 MET cc_start: 0.8234 (tpp) cc_final: 0.7957 (mtm) REVERT: A 758 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.3559 (pp) REVERT: B 46 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8771 (pp) REVERT: B 273 MET cc_start: 0.8689 (tpt) cc_final: 0.7995 (tpt) REVERT: B 386 ASN cc_start: 0.8380 (t0) cc_final: 0.7830 (t0) REVERT: B 554 ARG cc_start: 0.7285 (tmm-80) cc_final: 0.6898 (ttt90) REVERT: B 572 MET cc_start: 0.6771 (tpt) cc_final: 0.6228 (tpp) REVERT: B 612 MET cc_start: 0.9237 (mmm) cc_final: 0.8913 (mmm) REVERT: B 736 ASP cc_start: 0.8220 (p0) cc_final: 0.7938 (p0) REVERT: B 758 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3271 (pp) REVERT: B 985 LEU cc_start: 0.9166 (pt) cc_final: 0.8621 (mp) REVERT: B 1047 SER cc_start: 0.8518 (p) cc_final: 0.8138 (m) outliers start: 77 outliers final: 66 residues processed: 312 average time/residue: 0.2270 time to fit residues: 113.4235 Evaluate side-chains 327 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 253 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1036 TYR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 99 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098536 restraints weight = 31605.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101847 restraints weight = 16116.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104050 restraints weight = 10745.153| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16690 Z= 0.184 Angle : 0.637 11.748 22910 Z= 0.307 Chirality : 0.043 0.210 2754 Planarity : 0.004 0.040 2922 Dihedral : 4.702 35.539 2406 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.84 % Allowed : 26.77 % Favored : 68.39 % 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: -1.10 (0.18), residues: 2216 helix: 1.13 (0.18), residues: 878 sheet: -1.70 (0.30), residues: 242 loop : -2.15 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 944 HIS 0.002 0.001 HIS B 857 PHE 0.027 0.001 PHE A 193 TYR 0.017 0.001 TYR A 301 ARG 0.004 0.000 ARG B 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.20 seconds wall clock time: 60 minutes 50.07 seconds (3650.07 seconds total)