Starting phenix.real_space_refine on Sat Feb 17 17:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/02_2024/7t6o_25721.pdb" } resolution = 2.6 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= 0.002 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 382": "OD1" <-> "OD2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 382": "OD1" <-> "OD2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 605": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 605": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 10.35, per 1000 atoms: 0.53 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.59, 143.59, 119.52, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.4 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.792A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.627A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.932A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.982A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix removed outlier: 3.693A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.587A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.547A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 585 through 608 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.744A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.794A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.108A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.519A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.633A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.504A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.003A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.912A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.983A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix removed outlier: 3.694A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.592A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 585 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.747A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.790A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.529A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.630A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.519A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.999A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.923A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.906A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.005A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.693A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 487 removed outlier: 4.278A pdb=" N PHE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.608A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.599A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 Processing helix chain 'C' and resid 585 through 608 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.759A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.793A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.629A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.927A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.941A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.846A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.985A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix removed outlier: 3.693A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.609A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 487 removed outlier: 4.284A pdb=" N PHE D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.618A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.546A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 Processing helix chain 'D' and resid 585 through 608 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.740A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.697A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.703A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1129 hydrogen bonds defined for protein. 3219 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: 6.37 Time building geometry restraints manager: 7.65 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: 6195 1.34 - 1.46: 4253 1.46 - 1.58: 9184 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.85e+00 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.81e+00 bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.337 1.367 -0.029 1.24e-02 6.50e+03 5.62e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.38e+00 bond pdb=" C VAL B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.38e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.00: 424 106.00 - 113.01: 10483 113.01 - 120.02: 7336 120.02 - 127.03: 8474 127.03 - 134.04: 247 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N GLU C 591 " pdb=" CA GLU C 591 " pdb=" CB GLU C 591 " ideal model delta sigma weight residual 110.28 117.34 -7.06 1.55e+00 4.16e-01 2.07e+01 angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.28 117.31 -7.03 1.55e+00 4.16e-01 2.06e+01 angle pdb=" N GLU D 591 " pdb=" CA GLU D 591 " pdb=" CB GLU D 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" N GLU B 591 " pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10669 17.04 - 34.07: 903 34.07 - 51.11: 168 51.11 - 68.15: 44 68.15 - 85.18: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET C 474 " pdb=" C MET C 474 " pdb=" N LEU C 475 " pdb=" CA LEU C 475 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA MET B 474 " pdb=" C MET B 474 " pdb=" N LEU B 475 " pdb=" CA LEU B 475 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA MET A 474 " pdb=" C MET A 474 " pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2716 0.074 - 0.148: 333 0.148 - 0.223: 19 0.223 - 0.297: 0 0.297 - 0.371: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 477 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.030 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5632 2.82 - 3.34: 18026 3.34 - 3.86: 34068 3.86 - 4.38: 40083 4.38 - 4.90: 67034 Nonbonded interactions: 164843 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.303 2.440 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.342 2.440 ... (remaining 164838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.790 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 50.100 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 0.057 19860 Z= 0.275 Angle : 0.793 8.831 26964 Z= 0.430 Chirality : 0.048 0.371 3072 Planarity : 0.007 0.065 3416 Dihedral : 14.057 85.182 7236 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.56 (0.15), residues: 2408 helix: -0.80 (0.11), residues: 1484 sheet: -1.14 (0.45), residues: 128 loop : -1.16 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 593 HIS 0.005 0.001 HIS D 201 PHE 0.022 0.002 PHE B 553 TYR 0.013 0.002 TYR A 623 ARG 0.015 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.237 Fit side-chains REVERT: A 233 GLU cc_start: 0.7625 (tt0) cc_final: 0.6999 (mm-30) REVERT: B 139 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6908 (mmm160) REVERT: B 233 GLU cc_start: 0.7624 (tt0) cc_final: 0.6993 (mm-30) REVERT: C 139 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6903 (mmm160) REVERT: C 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7003 (mm-30) REVERT: D 233 GLU cc_start: 0.7623 (tt0) cc_final: 0.6997 (mm-30) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 1.3608 time to fit residues: 564.5554 Evaluate side-chains 310 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 208 ASN A 587 GLN B 131 ASN B 208 ASN B 587 GLN C 131 ASN C 208 ASN C 587 GLN D 131 ASN D 208 ASN D 587 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.195 Angle : 0.500 5.927 26964 Z= 0.264 Chirality : 0.039 0.129 3072 Planarity : 0.005 0.042 3416 Dihedral : 4.114 15.787 2644 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.34 % Allowed : 6.82 % Favored : 90.84 % 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: 0.31 (0.16), residues: 2408 helix: 0.79 (0.13), residues: 1492 sheet: -1.15 (0.45), residues: 128 loop : -0.51 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.004 0.001 HIS D 258 PHE 0.019 0.002 PHE C 537 TYR 0.011 0.002 TYR A 555 ARG 0.005 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 321 time to evaluate : 2.114 Fit side-chains REVERT: A 35 ARG cc_start: 0.6974 (tpt90) cc_final: 0.6679 (tpt170) REVERT: A 38 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7229 (mtm) REVERT: A 491 MET cc_start: 0.7445 (tpp) cc_final: 0.7196 (tpt) REVERT: A 589 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7287 (ttm170) REVERT: B 35 ARG cc_start: 0.6992 (tpt90) cc_final: 0.6694 (tpt170) REVERT: B 38 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7244 (mtm) REVERT: B 129 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7468 (m-40) REVERT: B 139 ARG cc_start: 0.7316 (mtp180) cc_final: 0.7109 (mmm160) REVERT: B 491 MET cc_start: 0.7437 (tpp) cc_final: 0.7204 (tpt) REVERT: B 589 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7284 (ttm170) REVERT: C 35 ARG cc_start: 0.6988 (tpt90) cc_final: 0.6686 (tpt170) REVERT: C 38 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7253 (mtm) REVERT: C 139 ARG cc_start: 0.7305 (mtp180) cc_final: 0.7086 (mmm160) REVERT: C 589 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7305 (ttm170) REVERT: D 35 ARG cc_start: 0.6990 (tpt90) cc_final: 0.6694 (tpt170) REVERT: D 38 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7241 (mtm) REVERT: D 491 MET cc_start: 0.7461 (tpp) cc_final: 0.7187 (tpt) REVERT: D 589 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7287 (ttm170) outliers start: 49 outliers final: 1 residues processed: 353 average time/residue: 1.2577 time to fit residues: 501.2472 Evaluate side-chains 314 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 308 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.170 Angle : 0.468 5.848 26964 Z= 0.245 Chirality : 0.038 0.126 3072 Planarity : 0.004 0.039 3416 Dihedral : 3.883 14.456 2644 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.81 % Allowed : 10.54 % Favored : 87.64 % 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: 1.00 (0.17), residues: 2408 helix: 1.41 (0.13), residues: 1492 sheet: -1.22 (0.44), residues: 128 loop : -0.33 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.014 0.001 PHE C 537 TYR 0.009 0.001 TYR B 555 ARG 0.004 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 2.298 Fit side-chains REVERT: A 38 MET cc_start: 0.7684 (ttp) cc_final: 0.7439 (mtm) REVERT: A 129 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7570 (m-40) REVERT: A 491 MET cc_start: 0.7533 (tpp) cc_final: 0.7323 (tpt) REVERT: B 129 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7592 (m-40) REVERT: B 139 ARG cc_start: 0.7384 (mtp180) cc_final: 0.7167 (mmm160) REVERT: C 139 ARG cc_start: 0.7377 (mtp180) cc_final: 0.7140 (mmm160) REVERT: D 129 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7568 (m-40) REVERT: D 491 MET cc_start: 0.7528 (tpp) cc_final: 0.7322 (tpt) outliers start: 38 outliers final: 10 residues processed: 342 average time/residue: 1.4258 time to fit residues: 546.7792 Evaluate side-chains 317 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 304 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 0.0970 chunk 219 optimal weight: 0.7980 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 51 GLN A 131 ASN B 131 ASN C 51 GLN C 129 ASN C 131 ASN D 51 GLN D 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19860 Z= 0.156 Angle : 0.455 5.777 26964 Z= 0.238 Chirality : 0.038 0.124 3072 Planarity : 0.004 0.048 3416 Dihedral : 3.755 14.211 2644 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.72 % Allowed : 12.21 % Favored : 86.07 % 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: 1.32 (0.17), residues: 2408 helix: 1.66 (0.13), residues: 1500 sheet: -1.51 (0.43), residues: 136 loop : -0.12 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.001 PHE C 537 TYR 0.010 0.001 TYR D 555 ARG 0.005 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 317 time to evaluate : 2.276 Fit side-chains REVERT: A 129 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: A 578 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: B 129 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7674 (m-40) REVERT: B 139 ARG cc_start: 0.7405 (mtp180) cc_final: 0.7141 (mmm160) REVERT: B 323 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7979 (tmtt) REVERT: C 139 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7112 (mmm160) REVERT: D 129 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7607 (m-40) outliers start: 36 outliers final: 21 residues processed: 344 average time/residue: 1.2854 time to fit residues: 498.8025 Evaluate side-chains 332 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 129 ASN A 131 ASN B 51 GLN B 129 ASN B 131 ASN C 129 ASN C 131 ASN D 51 GLN D 129 ASN D 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19860 Z= 0.286 Angle : 0.540 5.972 26964 Z= 0.283 Chirality : 0.042 0.142 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.124 17.467 2644 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.05 % Allowed : 12.45 % Favored : 85.50 % 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: 1.16 (0.17), residues: 2408 helix: 1.53 (0.13), residues: 1492 sheet: -1.21 (0.46), residues: 128 loop : -0.24 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.012 0.002 PHE D 472 TYR 0.012 0.002 TYR B 555 ARG 0.009 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 317 time to evaluate : 2.324 Fit side-chains REVERT: A 129 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7770 (m110) REVERT: A 578 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: B 129 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7772 (m110) REVERT: B 139 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7122 (mmm160) REVERT: B 323 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8037 (tmtt) REVERT: C 139 ARG cc_start: 0.7459 (mtp180) cc_final: 0.7110 (mmm160) REVERT: D 129 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7728 (m110) outliers start: 43 outliers final: 22 residues processed: 349 average time/residue: 1.3064 time to fit residues: 513.1898 Evaluate side-chains 337 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 310 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 51 GLN A 129 ASN A 131 ASN B 129 ASN B 131 ASN C 51 GLN C 129 ASN C 131 ASN D 51 GLN D 129 ASN D 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.199 Angle : 0.492 5.871 26964 Z= 0.257 Chirality : 0.039 0.132 3072 Planarity : 0.004 0.044 3416 Dihedral : 3.952 15.506 2644 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.10 % Allowed : 12.36 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2408 helix: 1.70 (0.13), residues: 1492 sheet: -1.48 (0.44), residues: 136 loop : -0.08 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.004 0.001 HIS A 201 PHE 0.011 0.002 PHE C 537 TYR 0.011 0.001 TYR A 555 ARG 0.012 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 2.293 Fit side-chains REVERT: A 381 GLN cc_start: 0.5270 (tp40) cc_final: 0.4857 (mp10) REVERT: A 578 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: B 139 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7183 (mmm160) REVERT: B 323 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8027 (tmtt) REVERT: C 129 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7756 (m110) REVERT: C 139 ARG cc_start: 0.7475 (mtp180) cc_final: 0.7161 (mmt-90) REVERT: D 381 GLN cc_start: 0.5278 (tp40) cc_final: 0.4862 (mp10) outliers start: 44 outliers final: 28 residues processed: 342 average time/residue: 1.3064 time to fit residues: 502.5677 Evaluate side-chains 338 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 307 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 51 GLN A 129 ASN A 131 ASN B 51 GLN B 129 ASN B 131 ASN C 51 GLN C 129 ASN C 131 ASN D 51 GLN D 129 ASN D 131 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.163 Angle : 0.472 5.869 26964 Z= 0.245 Chirality : 0.038 0.125 3072 Planarity : 0.004 0.048 3416 Dihedral : 3.792 14.430 2644 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.67 % Allowed : 13.31 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.17), residues: 2408 helix: 1.85 (0.13), residues: 1492 sheet: -1.50 (0.43), residues: 136 loop : -0.02 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS C 201 PHE 0.011 0.001 PHE C 534 TYR 0.009 0.001 TYR D 555 ARG 0.013 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 2.173 Fit side-chains REVERT: A 381 GLN cc_start: 0.5251 (tp40) cc_final: 0.4847 (mp10) REVERT: B 129 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7795 (m110) REVERT: B 139 ARG cc_start: 0.7428 (mtp180) cc_final: 0.7139 (mmt-90) REVERT: B 323 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (tmtt) REVERT: C 139 ARG cc_start: 0.7425 (mtp180) cc_final: 0.7134 (mmm160) REVERT: D 381 GLN cc_start: 0.5258 (tp40) cc_final: 0.4851 (mp10) outliers start: 35 outliers final: 26 residues processed: 333 average time/residue: 1.2787 time to fit residues: 480.5492 Evaluate side-chains 336 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 308 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 147 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 129 ASN A 131 ASN B 51 GLN B 131 ASN C 129 ASN C 131 ASN D 51 GLN D 129 ASN D 131 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.172 Angle : 0.482 6.980 26964 Z= 0.249 Chirality : 0.038 0.126 3072 Planarity : 0.004 0.053 3416 Dihedral : 3.775 14.365 2644 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.62 % Allowed : 13.65 % Favored : 84.73 % 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: 1.61 (0.17), residues: 2408 helix: 1.89 (0.13), residues: 1496 sheet: -1.51 (0.43), residues: 136 loop : 0.03 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.004 0.001 HIS C 201 PHE 0.010 0.001 PHE C 534 TYR 0.015 0.001 TYR A 621 ARG 0.014 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 309 time to evaluate : 2.245 Fit side-chains REVERT: A 381 GLN cc_start: 0.5278 (tp40) cc_final: 0.4837 (mp10) REVERT: B 139 ARG cc_start: 0.7459 (mtp180) cc_final: 0.7166 (mmt-90) REVERT: B 323 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8001 (tmtt) REVERT: C 139 ARG cc_start: 0.7414 (mtp180) cc_final: 0.7120 (mmt-90) REVERT: D 381 GLN cc_start: 0.5284 (tp40) cc_final: 0.4842 (mp10) outliers start: 34 outliers final: 26 residues processed: 334 average time/residue: 1.2965 time to fit residues: 488.2657 Evaluate side-chains 332 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 0.0980 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 129 ASN A 131 ASN B 51 GLN B 131 ASN C 129 ASN C 131 ASN D 51 GLN D 129 ASN D 131 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.155 Angle : 0.478 8.018 26964 Z= 0.246 Chirality : 0.038 0.123 3072 Planarity : 0.004 0.056 3416 Dihedral : 3.703 14.136 2644 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.72 % Allowed : 13.74 % Favored : 84.54 % 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: 1.69 (0.17), residues: 2408 helix: 1.92 (0.13), residues: 1508 sheet: -1.49 (0.43), residues: 136 loop : 0.12 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE C 534 TYR 0.016 0.001 TYR C 621 ARG 0.015 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 314 time to evaluate : 2.112 Fit side-chains REVERT: A 233 GLU cc_start: 0.7639 (tt0) cc_final: 0.7025 (mm-30) REVERT: B 139 ARG cc_start: 0.7429 (mtp180) cc_final: 0.7150 (mmt-90) REVERT: B 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7015 (mm-30) REVERT: B 323 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7997 (tmtt) REVERT: C 139 ARG cc_start: 0.7420 (mtp180) cc_final: 0.7135 (mmt-90) REVERT: C 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7023 (mm-30) REVERT: C 466 MET cc_start: 0.8721 (mtt) cc_final: 0.8520 (mtt) REVERT: D 233 GLU cc_start: 0.7637 (tt0) cc_final: 0.7021 (mm-30) REVERT: D 381 GLN cc_start: 0.5265 (tp40) cc_final: 0.4820 (mp10) REVERT: D 466 MET cc_start: 0.8717 (mtt) cc_final: 0.8513 (mtt) outliers start: 36 outliers final: 26 residues processed: 339 average time/residue: 1.2547 time to fit residues: 479.4731 Evaluate side-chains 335 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 308 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9990 chunk 227 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.0030 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 129 ASN A 131 ASN B 131 ASN C 129 ASN C 131 ASN D 129 ASN D 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.148 Angle : 0.479 8.847 26964 Z= 0.245 Chirality : 0.038 0.122 3072 Planarity : 0.004 0.059 3416 Dihedral : 3.644 13.935 2644 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.43 % Allowed : 14.22 % Favored : 84.35 % 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: 1.72 (0.17), residues: 2408 helix: 1.95 (0.13), residues: 1512 sheet: -1.46 (0.43), residues: 136 loop : 0.08 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 593 HIS 0.003 0.001 HIS B 201 PHE 0.011 0.001 PHE C 534 TYR 0.017 0.001 TYR A 621 ARG 0.015 0.000 ARG B 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 308 time to evaluate : 2.165 Fit side-chains REVERT: A 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7020 (mm-30) REVERT: B 139 ARG cc_start: 0.7409 (mtp180) cc_final: 0.7124 (mmt-90) REVERT: B 233 GLU cc_start: 0.7636 (tt0) cc_final: 0.7009 (mm-30) REVERT: B 323 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8000 (tmtt) REVERT: C 139 ARG cc_start: 0.7406 (mtp180) cc_final: 0.7127 (mmt-90) REVERT: C 233 GLU cc_start: 0.7639 (tt0) cc_final: 0.7019 (mm-30) REVERT: D 233 GLU cc_start: 0.7637 (tt0) cc_final: 0.7017 (mm-30) REVERT: D 466 MET cc_start: 0.8696 (mtt) cc_final: 0.8496 (mtt) outliers start: 30 outliers final: 23 residues processed: 327 average time/residue: 1.2538 time to fit residues: 462.8242 Evaluate side-chains 323 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 299 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 51 GLN B 131 ASN C 51 GLN C 129 ASN C 131 ASN D 51 GLN D 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145492 restraints weight = 19572.252| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.03 r_work: 0.3422 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.187 Angle : 0.488 5.825 26964 Z= 0.255 Chirality : 0.039 0.130 3072 Planarity : 0.004 0.059 3416 Dihedral : 3.754 14.546 2644 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.43 % Allowed : 14.31 % Favored : 84.26 % 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: 1.65 (0.17), residues: 2408 helix: 1.91 (0.13), residues: 1500 sheet: -1.48 (0.43), residues: 136 loop : 0.07 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS D 201 PHE 0.015 0.002 PHE C 553 TYR 0.010 0.001 TYR A 555 ARG 0.015 0.000 ARG D 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8050.91 seconds wall clock time: 143 minutes 25.57 seconds (8605.57 seconds total)