Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:25:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u86_20678/03_2023/6u86_20678.pdb" } resolution = 4.0 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 680": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 680": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Residue "D GLU 716": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 20140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5035 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 11.14, per 1000 atoms: 0.55 Number of scatterers: 20140 At special positions: 0 Unit cell: (138.86, 138.86, 111.3, 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 116 16.00 O 3460 8.00 N 3384 7.00 C 13180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 64.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.581A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.966A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.540A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 561 removed outlier: 4.597A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 Processing helix chain 'A' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.613A pdb=" N ASN A 650 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.580A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.967A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.541A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.613A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 561 removed outlier: 4.597A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 651 removed outlier: 3.613A pdb=" N ASN B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.581A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.509A pdb=" N VAL C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.625A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.966A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.540A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 561 removed outlier: 4.596A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 551 " --> pdb=" O PHE C 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 Processing helix chain 'C' and resid 618 through 646 removed outlier: 3.658A pdb=" N VAL C 622 " --> pdb=" O PHE C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 removed outlier: 3.612A pdb=" N ASN C 650 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 4.193A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.686A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.642A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.960A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.582A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.510A pdb=" N VAL D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.624A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.967A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 377 through 414 removed outlier: 5.639A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 461 through 466 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.541A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.612A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 4.150A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 532 removed outlier: 4.167A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 561 removed outlier: 4.596A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 551 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 Processing helix chain 'D' and resid 618 through 646 removed outlier: 3.659A pdb=" N VAL D 622 " --> pdb=" O PHE D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 removed outlier: 3.614A pdb=" N ASN D 650 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 4.194A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 709 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 341 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 707 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 709 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 341 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 707 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.697A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU C 709 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 341 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 707 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.698A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU D 709 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 341 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL D 707 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3084 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: 5.95 Time building geometry restraints manager: 9.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6304 1.34 - 1.46: 4308 1.46 - 1.57: 9860 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 20652 Sorted by residual: bond pdb=" CB PRO B 377 " pdb=" CG PRO B 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO C 377 " pdb=" CG PRO C 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO A 377 " pdb=" CG PRO A 377 " ideal model delta sigma weight residual 1.506 1.450 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB PRO D 377 " pdb=" CG PRO D 377 " ideal model delta sigma weight residual 1.506 1.451 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CG LEU B 253 " pdb=" CD2 LEU B 253 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 ... (remaining 20647 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.56: 555 106.56 - 113.42: 11361 113.42 - 120.29: 7487 120.29 - 127.15: 8311 127.15 - 134.02: 294 Bond angle restraints: 28008 Sorted by residual: angle pdb=" N LEU C 513 " pdb=" CA LEU C 513 " pdb=" C LEU C 513 " ideal model delta sigma weight residual 114.64 110.87 3.77 1.52e+00 4.33e-01 6.14e+00 angle pdb=" N LEU B 513 " pdb=" CA LEU B 513 " pdb=" C LEU B 513 " ideal model delta sigma weight residual 114.64 110.88 3.76 1.52e+00 4.33e-01 6.12e+00 angle pdb=" N LEU D 513 " pdb=" CA LEU D 513 " pdb=" C LEU D 513 " ideal model delta sigma weight residual 114.64 110.88 3.76 1.52e+00 4.33e-01 6.12e+00 angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.64 110.90 3.74 1.52e+00 4.33e-01 6.05e+00 angle pdb=" CA LEU D 498 " pdb=" C LEU D 498 " pdb=" N PRO D 499 " ideal model delta sigma weight residual 120.81 118.94 1.87 8.60e-01 1.35e+00 4.71e+00 ... (remaining 28003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10924 17.58 - 35.16: 1046 35.16 - 52.75: 154 52.75 - 70.33: 12 70.33 - 87.91: 12 Dihedral angle restraints: 12148 sinusoidal: 4916 harmonic: 7232 Sorted by residual: dihedral pdb=" CA LEU C 534 " pdb=" C LEU C 534 " pdb=" N ARG C 535 " pdb=" CA ARG C 535 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU D 534 " pdb=" C LEU D 534 " pdb=" N ARG D 535 " pdb=" CA ARG D 535 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU A 534 " pdb=" C LEU A 534 " pdb=" N ARG A 535 " pdb=" CA ARG A 535 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 12145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1801 0.028 - 0.056: 850 0.056 - 0.084: 349 0.084 - 0.112: 123 0.112 - 0.140: 17 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA GLN C 520 " pdb=" N GLN C 520 " pdb=" C GLN C 520 " pdb=" CB GLN C 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA GLN D 520 " pdb=" N GLN D 520 " pdb=" C GLN D 520 " pdb=" CB GLN D 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA GLN A 520 " pdb=" N GLN A 520 " pdb=" C GLN A 520 " pdb=" CB GLN A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3137 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 99 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C LEU A 99 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 99 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 100 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 99 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C LEU D 99 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU D 99 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 100 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 99 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU C 99 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU C 99 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 100 " -0.018 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2293 2.74 - 3.28: 22154 3.28 - 3.82: 32317 3.82 - 4.36: 37178 4.36 - 4.90: 62184 Nonbonded interactions: 156126 Sorted by model distance: nonbonded pdb=" OD1 ASP A 159 " pdb=" N GLU A 160 " model vdw 2.198 2.520 nonbonded pdb=" OD1 ASP B 159 " pdb=" N GLU B 160 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASP C 159 " pdb=" N GLU C 160 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASP D 159 " pdb=" N GLU D 160 " model vdw 2.199 2.520 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.237 2.440 ... (remaining 156121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13180 2.51 5 N 3384 2.21 5 O 3460 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: 1.720 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: 0.020 Extract box with map and model: 6.930 Check model and map are aligned: 0.290 Process input model: 51.070 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.007 0.056 20652 Z= 0.431 Angle : 0.664 5.634 28008 Z= 0.375 Chirality : 0.039 0.140 3140 Planarity : 0.004 0.035 3468 Dihedral : 13.343 87.911 7468 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.88 (0.14), residues: 2432 helix: -2.06 (0.11), residues: 1488 sheet: None (None), residues: 0 loop : -3.30 (0.17), residues: 944 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 514 average time/residue: 0.3443 time to fit residues: 263.2614 Evaluate side-chains 287 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 283 time to evaluate : 2.447 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1758 time to fit residues: 4.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 316 GLN A 452 GLN A 530 GLN B 154 ASN B 452 GLN B 530 GLN C 154 ASN C 452 GLN C 530 GLN D 154 ASN D 452 GLN D 530 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20652 Z= 0.193 Angle : 0.616 8.685 28008 Z= 0.301 Chirality : 0.039 0.164 3140 Planarity : 0.004 0.038 3468 Dihedral : 4.197 20.331 2696 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.70 (0.16), residues: 2432 helix: 0.46 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -2.01 (0.18), residues: 936 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 412 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 29 residues processed: 441 average time/residue: 0.2868 time to fit residues: 200.1824 Evaluate side-chains 332 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 303 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1847 time to fit residues: 13.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 221 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 178 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 154 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 154 ASN B 316 GLN B 413 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 154 ASN C 316 GLN C 413 HIS D 148 ASN D 154 ASN D 413 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 20652 Z= 0.148 Angle : 0.578 9.482 28008 Z= 0.274 Chirality : 0.037 0.128 3140 Planarity : 0.003 0.033 3468 Dihedral : 3.806 16.721 2696 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.50 (0.17), residues: 2432 helix: 1.38 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -1.49 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 394 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 415 average time/residue: 0.2728 time to fit residues: 185.4510 Evaluate side-chains 348 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 2.515 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1808 time to fit residues: 10.3114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20652 Z= 0.166 Angle : 0.575 9.921 28008 Z= 0.271 Chirality : 0.037 0.139 3140 Planarity : 0.003 0.036 3468 Dihedral : 3.674 16.082 2696 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.83 (0.17), residues: 2432 helix: 1.58 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -1.23 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 353 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 47 residues processed: 400 average time/residue: 0.2644 time to fit residues: 175.0074 Evaluate side-chains 364 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 317 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.1918 time to fit residues: 20.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.7980 chunk 133 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.3980 chunk 211 optimal weight: 0.0980 chunk 59 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 316 GLN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 20652 Z= 0.133 Angle : 0.594 12.471 28008 Z= 0.269 Chirality : 0.036 0.136 3140 Planarity : 0.003 0.035 3468 Dihedral : 3.519 15.578 2696 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.99 (0.17), residues: 2432 helix: 1.72 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.05 (0.18), residues: 960 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 370 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 393 average time/residue: 0.2808 time to fit residues: 181.8995 Evaluate side-chains 334 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 310 time to evaluate : 2.502 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1856 time to fit residues: 11.9599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.0040 chunk 212 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 0.0010 chunk 58 optimal weight: 0.3980 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 0.0060 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 123 optimal weight: 0.0670 overall best weight: 0.0552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN C 438 HIS C 639 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 20652 Z= 0.126 Angle : 0.583 11.855 28008 Z= 0.261 Chirality : 0.037 0.215 3140 Planarity : 0.003 0.033 3468 Dihedral : 3.324 14.293 2696 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.03 (0.17), residues: 2432 helix: 1.72 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -0.99 (0.18), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 363 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 385 average time/residue: 0.2898 time to fit residues: 178.7249 Evaluate side-chains 343 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 322 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1828 time to fit residues: 10.4200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 134 optimal weight: 0.0870 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 0.0010 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 143 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS C 127 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 20652 Z= 0.136 Angle : 0.588 11.156 28008 Z= 0.262 Chirality : 0.036 0.125 3140 Planarity : 0.003 0.031 3468 Dihedral : 3.234 14.893 2696 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.15 (0.17), residues: 2432 helix: 1.83 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -0.95 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 367 average time/residue: 0.2776 time to fit residues: 165.9999 Evaluate side-chains 335 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 324 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1768 time to fit residues: 7.1163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.0570 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 639 ASN B 154 ASN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 20652 Z= 0.187 Angle : 0.624 10.996 28008 Z= 0.281 Chirality : 0.038 0.200 3140 Planarity : 0.003 0.030 3468 Dihedral : 3.401 15.277 2696 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.17 (0.17), residues: 2432 helix: 1.84 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -0.98 (0.18), residues: 944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 342 average time/residue: 0.2969 time to fit residues: 163.6092 Evaluate side-chains 331 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2088 time to fit residues: 12.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN B 154 ASN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN C 154 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20652 Z= 0.298 Angle : 0.699 11.592 28008 Z= 0.326 Chirality : 0.041 0.249 3140 Planarity : 0.003 0.031 3468 Dihedral : 3.940 16.464 2696 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.82 (0.17), residues: 2432 helix: 1.57 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -1.15 (0.18), residues: 944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 2.518 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 320 average time/residue: 0.2714 time to fit residues: 143.0800 Evaluate side-chains 300 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 2.459 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1758 time to fit residues: 9.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20652 Z= 0.280 Angle : 0.693 10.093 28008 Z= 0.321 Chirality : 0.041 0.253 3140 Planarity : 0.003 0.029 3468 Dihedral : 3.996 15.921 2696 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.80 (0.17), residues: 2432 helix: 1.52 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.04 (0.19), residues: 960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 292 time to evaluate : 2.504 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 297 average time/residue: 0.2531 time to fit residues: 126.8323 Evaluate side-chains 280 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 273 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1561 time to fit residues: 4.6531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093580 restraints weight = 42101.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096060 restraints weight = 23240.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097746 restraints weight = 15162.004| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20652 Z= 0.204 Angle : 0.667 12.610 28008 Z= 0.301 Chirality : 0.039 0.243 3140 Planarity : 0.003 0.029 3468 Dihedral : 3.803 17.412 2696 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.92 (0.17), residues: 2432 helix: 1.61 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -0.99 (0.19), residues: 960 Sorry: There was an error with writing 6u86_20678_real_space_refined_001.eff. [Errno 28] No space left on device