Starting phenix.real_space_refine (version: dev) on Tue Dec 13 16:33:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/12_2022/7bx8_30236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/12_2022/7bx8_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_30236/12_2022/7bx8_30236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/12_2022/7bx8_30236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/12_2022/7bx8_30236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/12_2022/7bx8_30236.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 9.60, per 1000 atoms: 0.59 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: 6.88 Conformation dependent library (CDL) restraints added in 2.6 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: 1.16 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: 5.74 Time building geometry restraints manager: 7.37 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 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. 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.060 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 44.620 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 % 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 *********************** 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 : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 387 average time/residue: 0.2682 time to fit residues: 156.8207 Evaluate side-chains 266 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1375 time to fit residues: 3.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 60 GLN B 112 ASN B 321 ASN B 431 GLN B1013 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16690 Z= 0.211 Angle : 0.694 12.966 22910 Z= 0.346 Chirality : 0.045 0.207 2754 Planarity : 0.006 0.068 2922 Dihedral : 5.415 25.114 2400 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 3.98 % 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: -0.53 (0.16), residues: 866 sheet: -2.32 (0.35), residues: 198 loop : -2.81 (0.17), residues: 1152 *********************** 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 344 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 280 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 320 average time/residue: 0.2646 time to fit residues: 130.7843 Evaluate side-chains 280 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 243 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1507 time to fit residues: 13.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 216 optimal weight: 0.0870 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 57 ASN B1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2262 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= 0.238 Angle : 0.659 11.712 22910 Z= 0.325 Chirality : 0.044 0.199 2754 Planarity : 0.005 0.048 2922 Dihedral : 4.943 23.373 2400 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 3.11 % 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: -1.96 (0.17), residues: 2216 helix: 0.26 (0.17), residues: 880 sheet: -2.08 (0.36), residues: 198 loop : -2.53 (0.17), residues: 1138 *********************** 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 312 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 17 residues processed: 297 average time/residue: 0.2511 time to fit residues: 116.9352 Evaluate side-chains 261 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1501 time to fit residues: 7.7183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 200 optimal weight: 0.0050 chunk 212 optimal weight: 0.8980 chunk 104 optimal weight: 0.0770 chunk 190 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A1013 GLN B 393 GLN B1013 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16690 Z= 0.159 Angle : 0.620 11.892 22910 Z= 0.302 Chirality : 0.043 0.226 2754 Planarity : 0.004 0.042 2922 Dihedral : 4.679 23.141 2400 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 3.42 % 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: -1.54 (0.18), residues: 2216 helix: 0.72 (0.18), residues: 870 sheet: -1.89 (0.34), residues: 214 loop : -2.34 (0.18), residues: 1132 *********************** 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 328 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 273 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 23 residues processed: 311 average time/residue: 0.2493 time to fit residues: 122.9305 Evaluate side-chains 274 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 251 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1557 time to fit residues: 9.5918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 3 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 483 GLN A 610 ASN B 610 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 16690 Z= 0.419 Angle : 0.741 10.870 22910 Z= 0.369 Chirality : 0.047 0.205 2754 Planarity : 0.005 0.045 2922 Dihedral : 4.926 22.240 2400 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 4.29 % 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: -1.63 (0.18), residues: 2216 helix: 0.58 (0.17), residues: 886 sheet: -1.92 (0.33), residues: 222 loop : -2.39 (0.18), residues: 1108 *********************** 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 319 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 250 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 48 residues processed: 290 average time/residue: 0.2358 time to fit residues: 109.1295 Evaluate side-chains 279 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 231 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1436 time to fit residues: 15.4963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2961 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= 0.231 Angle : 0.649 11.090 22910 Z= 0.314 Chirality : 0.044 0.191 2754 Planarity : 0.004 0.041 2922 Dihedral : 4.745 22.306 2400 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 2.48 % 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: -1.37 (0.18), residues: 2216 helix: 0.86 (0.17), residues: 888 sheet: -1.80 (0.32), residues: 226 loop : -2.30 (0.18), residues: 1102 *********************** 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 304 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 288 average time/residue: 0.2399 time to fit residues: 110.0771 Evaluate side-chains 259 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1561 time to fit residues: 8.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 212 optimal weight: 0.0040 chunk 132 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16690 Z= 0.205 Angle : 0.641 10.749 22910 Z= 0.310 Chirality : 0.043 0.191 2754 Planarity : 0.004 0.041 2922 Dihedral : 4.623 23.513 2400 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 2.05 % 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: -1.26 (0.18), residues: 2216 helix: 0.93 (0.18), residues: 892 sheet: -1.70 (0.32), residues: 228 loop : -2.23 (0.19), residues: 1096 *********************** 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 287 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 275 average time/residue: 0.2416 time to fit residues: 105.0268 Evaluate side-chains 260 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 244 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2056 time to fit residues: 7.9885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 483 GLN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16690 Z= 0.200 Angle : 0.652 11.872 22910 Z= 0.313 Chirality : 0.044 0.168 2754 Planarity : 0.004 0.040 2922 Dihedral : 4.558 23.063 2400 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.43 % 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: -1.19 (0.18), residues: 2216 helix: 0.93 (0.18), residues: 892 sheet: -1.61 (0.32), residues: 228 loop : -2.16 (0.19), residues: 1096 *********************** 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 277 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 254 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 270 average time/residue: 0.2394 time to fit residues: 102.4891 Evaluate side-chains 258 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1652 time to fit residues: 6.9397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 0.0070 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16690 Z= 0.237 Angle : 0.664 10.806 22910 Z= 0.318 Chirality : 0.044 0.222 2754 Planarity : 0.004 0.042 2922 Dihedral : 4.549 22.611 2400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2216 helix: 1.01 (0.18), residues: 892 sheet: -1.62 (0.31), residues: 238 loop : -2.14 (0.19), residues: 1086 *********************** 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 279 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 258 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 268 average time/residue: 0.2535 time to fit residues: 108.7875 Evaluate side-chains 261 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1619 time to fit residues: 6.2304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 6.9990 chunk 127 optimal weight: 0.0370 chunk 99 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 219 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.0170 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 16690 Z= 0.160 Angle : 0.653 10.855 22910 Z= 0.309 Chirality : 0.043 0.160 2754 Planarity : 0.004 0.038 2922 Dihedral : 4.405 22.617 2400 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2216 helix: 1.14 (0.18), residues: 880 sheet: -1.37 (0.32), residues: 228 loop : -2.06 (0.19), residues: 1108 ********************** 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 286 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 281 average time/residue: 0.2421 time to fit residues: 109.2850 Evaluate side-chains 260 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 254 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1547 time to fit residues: 4.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 6.9990 chunk 53 optimal weight: 0.0070 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.105233 restraints weight = 31803.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108860 restraints weight = 16108.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111252 restraints weight = 10760.843| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16690 Z= 0.172 Angle : 0.656 10.999 22910 Z= 0.313 Chirality : 0.043 0.155 2754 Planarity : 0.004 0.038 2922 Dihedral : 4.332 23.029 2400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2216 helix: 1.19 (0.18), residues: 878 sheet: -1.39 (0.32), residues: 232 loop : -2.06 (0.18), residues: 1106 =============================================================================== Job complete usr+sys time: 3118.57 seconds wall clock time: 57 minutes 28.47 seconds (3448.47 seconds total)