Starting phenix.real_space_refine (version: dev) on Wed Feb 22 01:57:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2023/7bx8_30236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2023/7bx8_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_2023/7bx8_30236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2023/7bx8_30236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2023/7bx8_30236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bx8_30236/02_2023/7bx8_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 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-4877/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: 9.62, 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: 6.58 Conformation dependent library (CDL) restraints added in 2.7 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: 1.14 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: 6.14 Time building geometry restraints manager: 7.10 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: 0.710 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: 5.120 Check model and map are aligned: 0.250 Process input model: 44.620 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.250 ------------------------------------------------------------------------------- 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 : 1.832 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: 0.2708 time to fit residues: 158.5362 Evaluate side-chains 266 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1416 time to fit residues: 3.8531 ------------------------------------------------------------------------------- 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 12.967 22910 Z= 0.346 Chirality : 0.045 0.207 2754 Planarity : 0.006 0.068 2922 Dihedral : 5.415 25.115 2400 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.64 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 : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 320 average time/residue: 0.2622 time to fit residues: 129.5657 Evaluate side-chains 280 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 243 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1498 time to fit residues: 12.8544 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 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: 2.5588 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16690 Z= 0.248 Angle : 0.664 11.695 22910 Z= 0.328 Chirality : 0.044 0.200 2754 Planarity : 0.005 0.049 2922 Dihedral : 4.959 23.340 2400 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2216 helix: 0.25 (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 316 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 265 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 19 residues processed: 300 average time/residue: 0.2493 time to fit residues: 117.3944 Evaluate side-chains 262 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1529 time to fit residues: 8.0025 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 190 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.2541 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= 0.201 Angle : 0.638 11.560 22910 Z= 0.312 Chirality : 0.044 0.236 2754 Planarity : 0.004 0.047 2922 Dihedral : 4.785 23.084 2400 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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: -1.67 (0.18), residues: 2216 helix: 0.57 (0.17), residues: 888 sheet: -2.06 (0.34), residues: 218 loop : -2.41 (0.18), residues: 1110 *********************** 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 332 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 263 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 26 residues processed: 307 average time/residue: 0.2426 time to fit residues: 118.1558 Evaluate side-chains 268 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1474 time to fit residues: 9.6255 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 87 optimal weight: 0.4980 chunk 181 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 610 ASN B 610 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 16690 Z= 0.401 Angle : 0.732 11.504 22910 Z= 0.363 Chirality : 0.047 0.203 2754 Planarity : 0.005 0.045 2922 Dihedral : 4.986 22.586 2400 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 4.10 % 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: -1.67 (0.18), residues: 2216 helix: 0.55 (0.17), residues: 888 sheet: -1.96 (0.33), residues: 222 loop : -2.41 (0.18), residues: 1106 *********************** 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: 66 poor density : 253 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 45 residues processed: 288 average time/residue: 0.2457 time to fit residues: 112.5782 Evaluate side-chains 285 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1544 time to fit residues: 15.7468 ------------------------------------------------------------------------------- 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: 10.0000 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 40.0000 chunk 52 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B1013 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 16690 Z= 0.243 Angle : 0.650 10.558 22910 Z= 0.316 Chirality : 0.044 0.192 2754 Planarity : 0.004 0.043 2922 Dihedral : 4.823 22.679 2400 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 2.98 % 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: -1.44 (0.18), residues: 2216 helix: 0.79 (0.17), residues: 890 sheet: -1.83 (0.31), residues: 238 loop : -2.33 (0.19), residues: 1088 *********************** 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 309 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 261 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 292 average time/residue: 0.2450 time to fit residues: 114.3919 Evaluate side-chains 260 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1950 time to fit residues: 10.3690 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 132 optimal weight: 0.0040 chunk 129 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.1798 ------------------------------------------------------------------------------- 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 B1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 16690 Z= 0.278 Angle : 0.672 9.899 22910 Z= 0.328 Chirality : 0.045 0.194 2754 Planarity : 0.004 0.048 2922 Dihedral : 4.777 23.898 2400 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 2.42 % 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: -1.42 (0.18), residues: 2216 helix: 0.85 (0.17), residues: 888 sheet: -1.84 (0.31), residues: 238 loop : -2.35 (0.19), residues: 1090 *********************** 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 293 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 254 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 276 average time/residue: 0.2476 time to fit residues: 108.1821 Evaluate side-chains 263 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 2.546 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1491 time to fit residues: 8.7555 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 0.0570 chunk 104 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 B1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3203 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= 0.192 Angle : 0.642 10.612 22910 Z= 0.310 Chirality : 0.043 0.188 2754 Planarity : 0.004 0.041 2922 Dihedral : 4.629 23.242 2400 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % 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: -1.22 (0.18), residues: 2216 helix: 0.99 (0.18), residues: 890 sheet: -1.70 (0.31), residues: 238 loop : -2.24 (0.19), residues: 1088 *********************** 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 289 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 267 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 281 average time/residue: 0.2483 time to fit residues: 110.1667 Evaluate side-chains 263 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1474 time to fit residues: 5.9070 ------------------------------------------------------------------------------- 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: 5.9990 chunk 185 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 0.2980 chunk 86 optimal weight: 0.0970 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.3301 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= 0.210 Angle : 0.659 10.855 22910 Z= 0.316 Chirality : 0.044 0.219 2754 Planarity : 0.004 0.053 2922 Dihedral : 4.574 22.882 2400 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 0.93 % 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: -1.14 (0.18), residues: 2216 helix: 1.03 (0.18), residues: 892 sheet: -1.61 (0.31), residues: 238 loop : -2.17 (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 274 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 259 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 266 average time/residue: 0.2466 time to fit residues: 104.0743 Evaluate side-chains 257 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1681 time to fit residues: 5.2143 ------------------------------------------------------------------------------- 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: 0.0050 chunk 99 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 174 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.7576 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16690 Z= 0.175 Angle : 0.658 11.339 22910 Z= 0.312 Chirality : 0.043 0.212 2754 Planarity : 0.004 0.045 2922 Dihedral : 4.474 22.518 2400 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.87 % 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: -1.04 (0.18), residues: 2216 helix: 1.07 (0.18), residues: 892 sheet: -1.49 (0.32), residues: 232 loop : -2.10 (0.19), residues: 1092 ********************** 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 281 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 267 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 274 average time/residue: 0.2464 time to fit residues: 107.1510 Evaluate side-chains 261 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 254 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1662 time to fit residues: 4.9650 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 0.0570 chunk 73 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 153 optimal weight: 0.0170 overall best weight: 1.8740 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101574 restraints weight = 31895.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105025 restraints weight = 16410.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107376 restraints weight = 11065.830| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3484 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= 0.214 Angle : 0.676 11.986 22910 Z= 0.324 Chirality : 0.044 0.204 2754 Planarity : 0.004 0.044 2922 Dihedral : 4.463 23.639 2400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.81 % 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: -1.05 (0.18), residues: 2216 helix: 1.04 (0.18), residues: 894 sheet: -1.45 (0.31), residues: 242 loop : -2.10 (0.19), residues: 1080 =============================================================================== Job complete usr+sys time: 3052.76 seconds wall clock time: 56 minutes 2.07 seconds (3362.07 seconds total)