Starting phenix.real_space_refine on Sun Mar 17 06:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sti_25429/03_2024/7sti_25429_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3406 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 8587 2.51 5 N 2326 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6585 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 770} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6570 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 769} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 7.18, per 1000 atoms: 0.53 Number of scatterers: 13531 At special positions: 0 Unit cell: (122.04, 105.84, 180.36, 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 110 16.00 O 2508 8.00 N 2326 7.00 C 8587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 682 " - pdb=" SG CYS B 685 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.02 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 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: 5.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 34 sheets defined 13.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.559A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.608A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.638A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.720A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 688 through 714 removed outlier: 3.796A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'B' and resid 17 through 24 removed outlier: 4.017A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.645A pdb=" N ASP B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 324 through 329 removed outlier: 4.299A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.905A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.169A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 688 through 712 removed outlier: 3.851A pdb=" N LEU B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 709 " --> pdb=" O PHE B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 869 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.089A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.733A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.842A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.842A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 94 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 63 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 96 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 8.546A pdb=" N LYS A 310 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE A 336 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS A 312 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 319 removed outlier: 6.282A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.347A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.752A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.274A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.989A pdb=" N GLY A 778 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 819 through 822 Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 862 removed outlier: 3.554A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 880 through 881 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.556A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 145 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 119 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 147 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.066A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.807A pdb=" N SER B 339 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 321 removed outlier: 6.807A pdb=" N SER B 339 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLU B 316 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N ILE B 341 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLU B 318 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.652A pdb=" N THR B 560 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 590 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 598 through 605 removed outlier: 6.741A pdb=" N LYS B 614 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER B 603 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 612 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.501A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.501A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 803 " --> pdb=" O TYR B 779 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 818 through 822 Processing sheet with id=AD7, first strand: chain 'B' and resid 856 through 862 removed outlier: 3.613A pdb=" N SER B 883 " --> pdb=" O ARG B 850 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 825 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: 4.74 Time building geometry restraints manager: 5.75 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: 4432 1.34 - 1.46: 3280 1.46 - 1.58: 6013 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13859 Sorted by residual: bond pdb=" C TRP B 615 " pdb=" N LYS B 616 " ideal model delta sigma weight residual 1.327 1.275 0.052 1.71e-02 3.42e+03 9.10e+00 bond pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" C LEU B 360 " pdb=" N ILE B 361 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.21e+00 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.20e-02 6.94e+03 1.73e+00 bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.29e-02 6.01e+03 1.50e+00 ... (remaining 13854 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.55: 309 105.55 - 112.66: 7280 112.66 - 119.77: 4428 119.77 - 126.88: 6549 126.88 - 133.99: 213 Bond angle restraints: 18779 Sorted by residual: angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 111.24 104.00 7.24 1.38e+00 5.25e-01 2.76e+01 angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 112.41 105.74 6.67 1.30e+00 5.92e-01 2.63e+01 angle pdb=" N GLY B 347 " pdb=" CA GLY B 347 " pdb=" C GLY B 347 " ideal model delta sigma weight residual 114.92 108.82 6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" C PRO A 307 " pdb=" N CYS A 308 " pdb=" CA CYS A 308 " ideal model delta sigma weight residual 121.80 131.87 -10.07 2.44e+00 1.68e-01 1.70e+01 angle pdb=" N GLY B 650 " pdb=" CA GLY B 650 " pdb=" C GLY B 650 " ideal model delta sigma weight residual 115.67 109.90 5.77 1.59e+00 3.96e-01 1.31e+01 ... (remaining 18774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7530 17.10 - 34.20: 712 34.20 - 51.30: 131 51.30 - 68.39: 25 68.39 - 85.49: 15 Dihedral angle restraints: 8413 sinusoidal: 3513 harmonic: 4900 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 176.70 -83.70 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 62 " pdb=" CB CYS C 62 " ideal model delta sinusoidal sigma weight residual 93.00 14.93 78.07 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -151.89 65.89 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 8410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1448 0.041 - 0.081: 413 0.081 - 0.122: 158 0.122 - 0.162: 16 0.162 - 0.203: 2 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU B 350 " pdb=" CB LEU B 350 " pdb=" CD1 LEU B 350 " pdb=" CD2 LEU B 350 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2034 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 308 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 309 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 455 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASN B 455 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 455 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 456 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 829 " 0.021 2.00e-02 2.50e+03 1.73e-02 4.47e+00 pdb=" CG HIS B 829 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS B 829 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 829 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 829 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 829 " 0.014 2.00e-02 2.50e+03 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 12156 3.16 - 3.74: 23419 3.74 - 4.32: 32215 4.32 - 4.90: 49919 Nonbonded interactions: 117941 Sorted by model distance: nonbonded pdb=" OE2 GLU A 698 " pdb=" OH TYR B 144 " model vdw 2.001 2.440 nonbonded pdb=" O LYS B 557 " pdb=" OG1 THR B 560 " model vdw 2.094 2.440 nonbonded pdb=" OD1 ASP B 812 " pdb=" OG SER B 890 " model vdw 2.105 2.440 nonbonded pdb=" O LYS B 557 " pdb=" OG1 THR B 590 " model vdw 2.111 2.440 nonbonded pdb=" OG SER B 50 " pdb=" O ASP B 74 " model vdw 2.130 2.440 ... (remaining 117936 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' and (resid 3 through 518 or resid 528 through 712 or resid 756 throug \ h 905)) selection = (chain 'B' and (resid 3 through 314 or resid 317 through 346 or resid 351 throug \ h 539 or resid 547 through 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.690 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.004 0.052 13859 Z= 0.237 Angle : 0.669 10.074 18779 Z= 0.372 Chirality : 0.043 0.203 2037 Planarity : 0.004 0.080 2427 Dihedral : 13.500 85.493 5137 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.80 % Favored : 92.02 % Rotamer: Outliers : 0.20 % Allowed : 0.26 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.35 (0.21), residues: 1642 helix: -1.06 (0.39), residues: 168 sheet: -0.27 (0.29), residues: 355 loop : -1.12 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 412 HIS 0.012 0.001 HIS B 829 PHE 0.019 0.002 PHE A 701 TYR 0.016 0.001 TYR A 579 ARG 0.006 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 MET cc_start: 0.9233 (mpp) cc_final: 0.9002 (mpp) REVERT: A 553 MET cc_start: 0.9380 (tpt) cc_final: 0.9093 (tpp) REVERT: B 72 LEU cc_start: 0.9616 (tp) cc_final: 0.9347 (tp) REVERT: B 410 GLN cc_start: 0.9103 (pt0) cc_final: 0.8815 (mp10) REVERT: B 852 TYR cc_start: 0.9623 (t80) cc_final: 0.9397 (p90) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.2434 time to fit residues: 24.2038 Evaluate side-chains 48 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13859 Z= 0.225 Angle : 0.606 9.891 18779 Z= 0.316 Chirality : 0.044 0.173 2037 Planarity : 0.004 0.081 2427 Dihedral : 4.804 26.623 1828 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.40 % Favored : 91.41 % Rotamer: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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 (0.21), residues: 1642 helix: -0.70 (0.38), residues: 170 sheet: -0.16 (0.29), residues: 346 loop : -1.08 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 551 HIS 0.009 0.001 HIS A 627 PHE 0.033 0.002 PHE B 701 TYR 0.016 0.001 TYR A 562 ARG 0.004 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9616 (tp) cc_final: 0.9360 (tp) REVERT: B 110 MET cc_start: 0.8965 (mmm) cc_final: 0.8687 (mmm) REVERT: B 852 TYR cc_start: 0.9614 (t80) cc_final: 0.9362 (p90) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.2410 time to fit residues: 20.2081 Evaluate side-chains 48 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 125 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 121 optimal weight: 0.7980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 470 ASN B 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13859 Z= 0.168 Angle : 0.574 9.804 18779 Z= 0.296 Chirality : 0.045 0.185 2037 Planarity : 0.004 0.082 2427 Dihedral : 4.619 25.654 1828 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.92 % Favored : 91.90 % Rotamer: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.23 (0.21), residues: 1642 helix: -0.78 (0.38), residues: 177 sheet: -0.28 (0.29), residues: 357 loop : -1.03 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 PHE 0.029 0.001 PHE B 701 TYR 0.010 0.001 TYR A 579 ARG 0.005 0.000 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9630 (tp) cc_final: 0.9374 (tp) REVERT: B 110 MET cc_start: 0.8959 (mmm) cc_final: 0.8591 (mmm) REVERT: B 410 GLN cc_start: 0.9052 (pt0) cc_final: 0.8711 (mp10) REVERT: B 442 MET cc_start: 0.9511 (mmp) cc_final: 0.9300 (mmm) REVERT: B 852 TYR cc_start: 0.9606 (t80) cc_final: 0.9330 (p90) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2411 time to fit residues: 22.6914 Evaluate side-chains 49 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13859 Z= 0.244 Angle : 0.594 9.733 18779 Z= 0.309 Chirality : 0.044 0.185 2037 Planarity : 0.004 0.083 2427 Dihedral : 4.716 25.481 1828 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.38 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1642 helix: -0.74 (0.40), residues: 169 sheet: -0.39 (0.28), residues: 348 loop : -1.02 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 PHE 0.029 0.002 PHE B 701 TYR 0.012 0.001 TYR A 562 ARG 0.007 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LEU cc_start: 0.9690 (tp) cc_final: 0.9423 (tp) REVERT: B 110 MET cc_start: 0.9032 (mmm) cc_final: 0.8662 (mmm) REVERT: B 852 TYR cc_start: 0.9622 (t80) cc_final: 0.9339 (p90) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2306 time to fit residues: 20.4785 Evaluate side-chains 48 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 40.0000 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 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 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13859 Z= 0.205 Angle : 0.572 9.691 18779 Z= 0.296 Chirality : 0.044 0.207 2037 Planarity : 0.004 0.085 2427 Dihedral : 4.669 24.874 1828 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.53 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1642 helix: -0.64 (0.39), residues: 171 sheet: -0.39 (0.28), residues: 347 loop : -0.99 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 PHE 0.030 0.001 PHE B 701 TYR 0.010 0.001 TYR A 507 ARG 0.008 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.8966 (mmp) cc_final: 0.8514 (mmm) REVERT: B 852 TYR cc_start: 0.9591 (t80) cc_final: 0.9263 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2361 time to fit residues: 20.6400 Evaluate side-chains 48 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 0.0570 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 3.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13859 Z= 0.233 Angle : 0.580 9.639 18779 Z= 0.300 Chirality : 0.044 0.188 2037 Planarity : 0.004 0.085 2427 Dihedral : 4.726 24.601 1828 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.44 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.23 (0.21), residues: 1642 helix: -0.59 (0.40), residues: 169 sheet: -0.49 (0.28), residues: 355 loop : -0.98 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 PHE 0.029 0.001 PHE B 701 TYR 0.012 0.001 TYR A 562 ARG 0.005 0.000 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.9048 (mmp) cc_final: 0.8494 (mmm) REVERT: B 110 MET cc_start: 0.9068 (mmm) cc_final: 0.8791 (mmm) REVERT: B 852 TYR cc_start: 0.9602 (t80) cc_final: 0.9273 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2284 time to fit residues: 19.7098 Evaluate side-chains 46 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 0.0040 chunk 100 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13859 Z= 0.268 Angle : 0.609 9.545 18779 Z= 0.316 Chirality : 0.044 0.182 2037 Planarity : 0.004 0.087 2427 Dihedral : 4.881 24.677 1828 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.20 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.33 (0.21), residues: 1642 helix: -0.69 (0.40), residues: 173 sheet: -0.56 (0.28), residues: 355 loop : -1.04 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 412 HIS 0.010 0.001 HIS A 627 PHE 0.029 0.002 PHE B 701 TYR 0.013 0.001 TYR A 562 ARG 0.007 0.001 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.9096 (mmp) cc_final: 0.8595 (mmm) REVERT: B 110 MET cc_start: 0.9094 (mmm) cc_final: 0.8834 (mmm) REVERT: B 553 MET cc_start: 0.9199 (mpp) cc_final: 0.8971 (mpp) REVERT: B 852 TYR cc_start: 0.9597 (t80) cc_final: 0.9279 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2369 time to fit residues: 20.4983 Evaluate side-chains 46 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13859 Z= 0.234 Angle : 0.592 9.511 18779 Z= 0.306 Chirality : 0.044 0.182 2037 Planarity : 0.004 0.088 2427 Dihedral : 4.893 25.436 1828 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.89 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1642 helix: -0.59 (0.40), residues: 172 sheet: -0.63 (0.28), residues: 359 loop : -1.03 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 412 HIS 0.010 0.001 HIS A 627 PHE 0.029 0.001 PHE B 701 TYR 0.012 0.001 TYR A 292 ARG 0.010 0.001 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9615 (mp) cc_final: 0.9299 (pt) REVERT: B 38 MET cc_start: 0.9127 (mmp) cc_final: 0.8590 (mmm) REVERT: B 110 MET cc_start: 0.9095 (mmm) cc_final: 0.8838 (mmm) REVERT: B 553 MET cc_start: 0.9193 (mpp) cc_final: 0.8924 (mpp) REVERT: B 852 TYR cc_start: 0.9581 (t80) cc_final: 0.9244 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2385 time to fit residues: 20.4605 Evaluate side-chains 45 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13859 Z= 0.174 Angle : 0.568 9.680 18779 Z= 0.292 Chirality : 0.044 0.178 2037 Planarity : 0.004 0.090 2427 Dihedral : 4.709 24.845 1828 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.28 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.23 (0.21), residues: 1642 helix: -0.62 (0.40), residues: 168 sheet: -0.47 (0.29), residues: 352 loop : -0.98 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 412 HIS 0.009 0.001 HIS A 627 PHE 0.031 0.001 PHE B 701 TYR 0.008 0.001 TYR A 507 ARG 0.005 0.000 ARG B 863 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9616 (mp) cc_final: 0.9304 (pt) REVERT: B 38 MET cc_start: 0.9054 (mmp) cc_final: 0.8486 (mmm) REVERT: B 110 MET cc_start: 0.9068 (mmm) cc_final: 0.8722 (mmm) REVERT: B 852 TYR cc_start: 0.9568 (t80) cc_final: 0.9227 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2399 time to fit residues: 20.6626 Evaluate side-chains 45 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 104 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13859 Z= 0.168 Angle : 0.559 9.635 18779 Z= 0.288 Chirality : 0.044 0.189 2037 Planarity : 0.004 0.092 2427 Dihedral : 4.640 24.415 1828 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.40 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -1.18 (0.22), residues: 1642 helix: -0.60 (0.40), residues: 167 sheet: -0.43 (0.29), residues: 358 loop : -0.95 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 412 HIS 0.008 0.001 HIS A 627 PHE 0.032 0.001 PHE B 701 TYR 0.009 0.001 TYR A 507 ARG 0.006 0.000 ARG B 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LEU cc_start: 0.9608 (mp) cc_final: 0.9286 (pt) REVERT: A 499 ASP cc_start: 0.9084 (m-30) cc_final: 0.8854 (t70) REVERT: B 38 MET cc_start: 0.9041 (mmp) cc_final: 0.8451 (mmm) REVERT: B 110 MET cc_start: 0.9058 (mmm) cc_final: 0.8713 (mmm) REVERT: B 455 ASN cc_start: 0.9152 (t0) cc_final: 0.8673 (m110) REVERT: B 852 TYR cc_start: 0.9565 (t80) cc_final: 0.9209 (p90) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2622 time to fit residues: 22.5893 Evaluate side-chains 48 residues out of total 1529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.035658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023663 restraints weight = 232274.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.024468 restraints weight = 136661.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.024992 restraints weight = 95781.493| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13859 Z= 0.240 Angle : 0.591 9.610 18779 Z= 0.304 Chirality : 0.044 0.185 2037 Planarity : 0.004 0.093 2427 Dihedral : 4.795 24.139 1828 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.38 % Favored : 90.50 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1642 helix: -0.61 (0.39), residues: 173 sheet: -0.55 (0.29), residues: 353 loop : -0.99 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 529 HIS 0.010 0.001 HIS A 627 PHE 0.031 0.002 PHE B 701 TYR 0.010 0.001 TYR A 562 ARG 0.006 0.001 ARG B 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.92 seconds wall clock time: 43 minutes 12.73 seconds (2592.73 seconds total)