Starting phenix.real_space_refine on Sat Feb 17 06:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qoe_18535/02_2024/8qoe_18535_neut.pdb" } resolution = 3.16 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5612 2.51 5 N 1456 2.21 5 O 1642 1.98 5 H 9072 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 399": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 486": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 495": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 571": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 316": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 399": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 486": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 495": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 571": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17816 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 8908 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 17, 'TRANS': 550} Chain: "A" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 8908 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 17, 'TRANS': 550} Time building chain proxies: 8.51, per 1000 atoms: 0.48 Number of scatterers: 17816 At special positions: 0 Unit cell: (110.21, 75.97, 133.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1642 8.00 N 1456 7.00 C 5612 6.00 H 9072 1.00 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: 14.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 64.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.659A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.501A pdb=" N LEU B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 64 through 109 removed outlier: 3.616A pdb=" N GLY B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.806A pdb=" N THR B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 117' Processing helix chain 'B' and resid 120 through 140 removed outlier: 3.556A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 164 through 210 Proline residue: B 175 - end of helix removed outlier: 3.549A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.578A pdb=" N ILE B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 274 removed outlier: 3.648A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.863A pdb=" N PHE B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.616A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.525A pdb=" N GLU B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.767A pdb=" N LYS B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 481 through 495 removed outlier: 3.587A pdb=" N ILE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.658A pdb=" N PHE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 3.502A pdb=" N LEU A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 109 removed outlier: 3.616A pdb=" N GLY A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.806A pdb=" N THR A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 117' Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.555A pdb=" N ARG A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix removed outlier: 3.550A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.577A pdb=" N ILE A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 274 removed outlier: 3.648A pdb=" N GLY A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.863A pdb=" N PHE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 322 removed outlier: 3.616A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.525A pdb=" N GLU A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.767A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.586A pdb=" N ILE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 572 through 577 Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.762A pdb=" N LYS B 358 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER B 347 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 397 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 417 through 421 removed outlier: 6.440A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP B 503 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 420 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 532 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 364 removed outlier: 6.762A pdb=" N LYS A 358 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER A 347 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 397 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.440A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP A 503 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 420 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 532 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 15.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2980 1.02 - 1.22: 6156 1.22 - 1.42: 3580 1.42 - 1.62: 5168 1.62 - 1.82: 66 Bond restraints: 17950 Sorted by residual: bond pdb=" CZ ARG B 316 " pdb=" NH2 ARG B 316 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 3.01e+02 bond pdb=" CZ ARG A 316 " pdb=" NH2 ARG A 316 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 3.00e+02 bond pdb=" CZ ARG A 126 " pdb=" NH2 ARG A 126 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 2.99e+02 bond pdb=" CZ ARG B 126 " pdb=" NH2 ARG B 126 " ideal model delta sigma weight residual 1.330 1.105 0.225 1.30e-02 5.92e+03 2.99e+02 bond pdb=" CZ ARG A 100 " pdb=" NH2 ARG A 100 " ideal model delta sigma weight residual 1.330 1.108 0.222 1.30e-02 5.92e+03 2.93e+02 ... (remaining 17945 not shown) Histogram of bond angle deviations from ideal: 97.00 - 105.54: 1026 105.54 - 114.07: 21836 114.07 - 122.61: 7534 122.61 - 131.15: 2150 131.15 - 139.69: 60 Bond angle restraints: 32606 Sorted by residual: angle pdb=" C GLU B 319 " pdb=" N ILE B 320 " pdb=" CA ILE B 320 " ideal model delta sigma weight residual 120.77 138.03 -17.26 1.31e+00 5.83e-01 1.74e+02 angle pdb=" C GLU A 319 " pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 120.77 138.00 -17.23 1.31e+00 5.83e-01 1.73e+02 angle pdb=" C ARG B 126 " pdb=" N VAL B 127 " pdb=" CA VAL B 127 " ideal model delta sigma weight residual 120.60 136.83 -16.23 1.29e+00 6.01e-01 1.58e+02 angle pdb=" C ARG A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 120.60 136.82 -16.22 1.29e+00 6.01e-01 1.58e+02 angle pdb=" C SER A 125 " pdb=" N ARG A 126 " pdb=" CA ARG A 126 " ideal model delta sigma weight residual 120.79 137.57 -16.78 1.39e+00 5.18e-01 1.46e+02 ... (remaining 32601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 7683 18.23 - 36.47: 385 36.47 - 54.70: 182 54.70 - 72.94: 72 72.94 - 91.17: 8 Dihedral angle restraints: 8330 sinusoidal: 4650 harmonic: 3680 Sorted by residual: dihedral pdb=" C ILE A 108 " pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" CB ILE A 108 " ideal model delta harmonic sigma weight residual -122.00 -145.09 23.09 0 2.50e+00 1.60e-01 8.53e+01 dihedral pdb=" C ILE B 108 " pdb=" N ILE B 108 " pdb=" CA ILE B 108 " pdb=" CB ILE B 108 " ideal model delta harmonic sigma weight residual -122.00 -145.06 23.06 0 2.50e+00 1.60e-01 8.51e+01 dihedral pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta harmonic sigma weight residual 122.80 144.56 -21.76 0 2.50e+00 1.60e-01 7.58e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 1216 0.209 - 0.417: 80 0.417 - 0.626: 120 0.626 - 0.835: 24 0.835 - 1.044: 14 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CA PHE B 115 " pdb=" N PHE B 115 " pdb=" C PHE B 115 " pdb=" CB PHE B 115 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CA TRP A 104 " pdb=" N TRP A 104 " pdb=" C TRP A 104 " pdb=" CB TRP A 104 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 1451 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 456 " -0.141 2.00e-02 2.50e+03 5.56e-02 9.26e+01 pdb=" CG TYR A 456 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 456 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 456 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 456 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 456 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 456 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 456 " -0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR A 456 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 456 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 TYR A 456 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR A 456 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 456 " 0.140 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR B 456 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 456 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 456 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 456 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 456 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 456 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 456 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 456 " -0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR B 456 " -0.065 2.00e-02 2.50e+03 pdb=" HE1 TYR B 456 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR B 456 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.124 2.00e-02 2.50e+03 5.15e-02 7.97e+01 pdb=" CG TYR B 26 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.097 2.00e-02 2.50e+03 pdb=" HD1 TYR B 26 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR B 26 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TYR B 26 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 26 " 0.012 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 102 1.87 - 2.55: 14700 2.55 - 3.24: 54678 3.24 - 3.92: 67689 3.92 - 4.60: 103767 Nonbonded interactions: 240936 Sorted by model distance: nonbonded pdb="HD21 ASN B 220 " pdb=" OE2 GLU A 411 " model vdw 1.188 1.850 nonbonded pdb=" OE2 GLU B 411 " pdb="HD21 ASN A 220 " model vdw 1.193 1.850 nonbonded pdb=" OE1 GLN B 208 " pdb=" HG SER A 428 " model vdw 1.233 1.850 nonbonded pdb=" HE1 MET B 271 " pdb="HD21 LEU A 62 " model vdw 1.265 2.440 nonbonded pdb=" HG2 GLU B 101 " pdb="HD11 ILE A 233 " model vdw 1.306 2.440 ... (remaining 240931 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' } 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 individual isotropic 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: 1.640 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: 0.310 Extract box with map and model: 6.590 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 59.620 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.019 0.225 8878 Z= 1.227 Angle : 2.440 17.379 12018 Z= 1.716 Chirality : 0.224 1.044 1454 Planarity : 0.014 0.124 1510 Dihedral : 14.312 91.170 3280 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.84 % Allowed : 4.70 % Favored : 94.47 % Cbeta Deviations : 11.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1132 helix: -1.37 (0.16), residues: 714 sheet: 0.06 (0.66), residues: 64 loop : -1.80 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.012 TRP A 104 HIS 0.009 0.003 HIS B 535 PHE 0.055 0.013 PHE B 286 TYR 0.114 0.020 TYR A 26 ARG 0.016 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.278 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 113 average time/residue: 0.5363 time to fit residues: 84.4273 Evaluate side-chains 61 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN A 61 ASN A 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8878 Z= 0.247 Angle : 0.678 6.011 12018 Z= 0.366 Chirality : 0.040 0.136 1454 Planarity : 0.004 0.036 1510 Dihedral : 6.024 44.480 1220 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.84 % Allowed : 8.46 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1132 helix: 0.39 (0.19), residues: 728 sheet: 0.09 (0.65), residues: 70 loop : -1.52 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 164 HIS 0.010 0.003 HIS B 561 PHE 0.014 0.002 PHE B 57 TYR 0.011 0.002 TYR A 437 ARG 0.003 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.471 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 revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.4160 time to fit residues: 43.3309 Evaluate side-chains 61 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8878 Z= 0.156 Angle : 0.534 6.405 12018 Z= 0.289 Chirality : 0.037 0.139 1454 Planarity : 0.003 0.032 1510 Dihedral : 5.074 20.810 1216 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.73 % Allowed : 9.19 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1132 helix: 1.02 (0.19), residues: 740 sheet: 0.33 (0.68), residues: 70 loop : -1.45 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.009 0.002 HIS B 561 PHE 0.013 0.001 PHE B 390 TYR 0.009 0.001 TYR B 570 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.4136 time to fit residues: 39.5541 Evaluate side-chains 59 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8878 Z= 0.221 Angle : 0.526 8.703 12018 Z= 0.281 Chirality : 0.037 0.137 1454 Planarity : 0.003 0.033 1510 Dihedral : 4.702 22.265 1216 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.94 % Allowed : 8.56 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1132 helix: 1.33 (0.19), residues: 744 sheet: 0.10 (0.66), residues: 70 loop : -1.33 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.008 0.002 HIS B 561 PHE 0.018 0.001 PHE A 390 TYR 0.008 0.001 TYR A 437 ARG 0.002 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.144 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.4666 time to fit residues: 38.5546 Evaluate side-chains 56 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 GLN A 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8878 Z= 0.213 Angle : 0.499 5.782 12018 Z= 0.269 Chirality : 0.037 0.137 1454 Planarity : 0.003 0.036 1510 Dihedral : 4.469 21.467 1216 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.04 % Allowed : 8.87 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1132 helix: 1.47 (0.19), residues: 744 sheet: -0.13 (0.64), residues: 70 loop : -1.34 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.008 0.002 HIS B 561 PHE 0.025 0.001 PHE B 390 TYR 0.008 0.001 TYR A 26 ARG 0.005 0.000 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 1.484 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 MET cc_start: 0.7600 (tpp) cc_final: 0.7361 (mmm) REVERT: B 501 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7720 (mtt) REVERT: A 501 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7758 (mtt) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.4582 time to fit residues: 39.4541 Evaluate side-chains 57 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8878 Z= 0.254 Angle : 0.504 5.702 12018 Z= 0.272 Chirality : 0.037 0.136 1454 Planarity : 0.003 0.037 1510 Dihedral : 4.381 21.782 1216 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.94 % Allowed : 9.19 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1132 helix: 1.44 (0.20), residues: 746 sheet: -0.38 (0.62), residues: 70 loop : -1.36 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.006 0.002 HIS B 561 PHE 0.015 0.001 PHE A 390 TYR 0.009 0.001 TYR A 570 ARG 0.002 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.428 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 REVERT: B 231 MET cc_start: 0.7627 (tpp) cc_final: 0.7387 (mmm) REVERT: B 501 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: A 501 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7704 (mtt) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.3813 time to fit residues: 32.0855 Evaluate side-chains 54 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8878 Z= 0.183 Angle : 0.477 6.455 12018 Z= 0.255 Chirality : 0.036 0.137 1454 Planarity : 0.003 0.037 1510 Dihedral : 4.269 20.522 1216 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.04 % Allowed : 9.29 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1132 helix: 1.60 (0.19), residues: 744 sheet: -0.45 (0.61), residues: 70 loop : -1.29 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.006 0.001 HIS B 561 PHE 0.016 0.001 PHE B 390 TYR 0.007 0.001 TYR A 570 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 1.648 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 REVERT: B 231 MET cc_start: 0.7564 (tpp) cc_final: 0.7338 (mmm) REVERT: B 501 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: A 501 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (mtt) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.3906 time to fit residues: 33.0199 Evaluate side-chains 57 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8878 Z= 0.157 Angle : 0.465 8.281 12018 Z= 0.247 Chirality : 0.035 0.136 1454 Planarity : 0.003 0.046 1510 Dihedral : 4.181 20.545 1216 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.73 % Allowed : 10.02 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1132 helix: 1.72 (0.19), residues: 744 sheet: -0.43 (0.61), residues: 70 loop : -1.21 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.006 0.001 HIS B 561 PHE 0.013 0.001 PHE A 390 TYR 0.007 0.001 TYR A 570 ARG 0.002 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.370 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 REVERT: B 231 MET cc_start: 0.7536 (tpp) cc_final: 0.7331 (mmm) REVERT: B 501 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: A 501 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7707 (mtt) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.3911 time to fit residues: 30.7204 Evaluate side-chains 54 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8878 Z= 0.157 Angle : 0.461 6.384 12018 Z= 0.245 Chirality : 0.035 0.136 1454 Planarity : 0.003 0.044 1510 Dihedral : 4.096 17.695 1216 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.94 % Allowed : 9.81 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1132 helix: 1.81 (0.19), residues: 744 sheet: -0.42 (0.61), residues: 70 loop : -1.12 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.006 0.001 HIS B 561 PHE 0.014 0.001 PHE B 390 TYR 0.006 0.001 TYR B 570 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 1.502 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 revert: symmetry clash REVERT: B 231 MET cc_start: 0.7539 (tpp) cc_final: 0.7329 (mmm) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.4903 time to fit residues: 37.3106 Evaluate side-chains 53 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 557 ARG Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8878 Z= 0.252 Angle : 0.493 8.139 12018 Z= 0.263 Chirality : 0.036 0.136 1454 Planarity : 0.003 0.035 1510 Dihedral : 4.110 19.194 1216 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.73 % Allowed : 10.13 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1132 helix: 1.66 (0.19), residues: 746 sheet: -0.56 (0.61), residues: 70 loop : -1.21 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.005 0.001 HIS B 561 PHE 0.015 0.001 PHE B 390 TYR 0.010 0.001 TYR A 570 ARG 0.003 0.000 ARG B 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.683 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 REVERT: B 231 MET cc_start: 0.7595 (tpp) cc_final: 0.7382 (mmm) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.4798 time to fit residues: 34.9726 Evaluate side-chains 52 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.106964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079326 restraints weight = 53750.189| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.08 r_work: 0.3197 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8878 Z= 0.133 Angle : 0.454 7.665 12018 Z= 0.239 Chirality : 0.035 0.138 1454 Planarity : 0.004 0.098 1510 Dihedral : 4.058 18.362 1216 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.52 % Allowed : 10.13 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1132 helix: 1.95 (0.20), residues: 742 sheet: -0.45 (0.61), residues: 70 loop : -1.07 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.006 0.001 HIS B 561 PHE 0.013 0.001 PHE B 390 TYR 0.006 0.001 TYR B 289 ARG 0.008 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.68 seconds wall clock time: 65 minutes 5.02 seconds (3905.02 seconds total)