Starting phenix.real_space_refine on Sat Sep 28 11:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6j_25716/09_2024/7t6j_25716.cif" } resolution = 3.2 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= 0.005 sd= 0.038 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. Time to flip 51 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.76, per 1000 atoms: 0.55 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 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 - 3.00 Amino acid : True - 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: 4.87 Conformation dependent library (CDL) restraints added in 2.5 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: 128 helices and 8 sheets defined 66.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 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 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.871A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.644A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.616A 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 193 through 197 removed outlier: 4.345A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.518A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.539A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.050A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.782A 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 308 removed outlier: 3.811A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.607A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.948A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.890A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.536A 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 removed outlier: 3.896A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.604A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.565A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 605 removed outlier: 4.114A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.567A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.696A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.531A 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 193 through 197 removed outlier: 4.342A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.531A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.520A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.039A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.770A 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 308 removed outlier: 3.811A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.614A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 402 removed outlier: 3.971A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.883A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.536A 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 removed outlier: 3.959A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.884A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 536 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.523A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 605 removed outlier: 4.067A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.560A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.863A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.642A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.517A 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 193 through 197 removed outlier: 4.331A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 210 through 222 removed outlier: 4.512A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.517A pdb=" N GLY C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.051A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.783A 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 308 removed outlier: 3.797A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.592A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 402 removed outlier: 3.962A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.891A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.538A 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 removed outlier: 3.968A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.597A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.878A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 536 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 605 removed outlier: 4.084A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.565A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.856A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.695A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.538A 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 193 through 197 removed outlier: 4.343A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 222 removed outlier: 4.528A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.511A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.046A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.771A 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 310 removed outlier: 3.809A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.595A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 402 removed outlier: 3.952A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.884A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.537A 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 removed outlier: 3.934A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.602A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.887A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.603A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 605 removed outlier: 4.104A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.810A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (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 268 removed outlier: 6.814A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (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 268 removed outlier: 6.813A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (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 268 removed outlier: 6.814A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1061 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 5.67 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: 6145 1.34 - 1.46: 4426 1.46 - 1.58: 9061 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" SD MET A 554 " pdb=" CE MET A 554 " ideal model delta sigma weight residual 1.791 1.728 0.063 2.50e-02 1.60e+03 6.44e+00 bond pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.23e-02 6.61e+03 6.31e+00 bond pdb=" C ILE D 404 " pdb=" N PRO D 405 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.15e+00 bond pdb=" C ILE B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 6.03e+00 bond pdb=" C ILE C 404 " pdb=" N PRO C 405 " ideal model delta sigma weight residual 1.335 1.369 -0.033 1.36e-02 5.41e+03 5.97e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 26539 3.69 - 7.38: 370 7.38 - 11.07: 40 11.07 - 14.75: 7 14.75 - 18.44: 8 Bond angle restraints: 26964 Sorted by residual: angle pdb=" CA LEU A 536 " pdb=" CB LEU A 536 " pdb=" CG LEU A 536 " ideal model delta sigma weight residual 116.30 134.74 -18.44 3.50e+00 8.16e-02 2.78e+01 angle pdb=" CA LEU C 536 " pdb=" CB LEU C 536 " pdb=" CG LEU C 536 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU D 536 " pdb=" CB LEU D 536 " pdb=" CG LEU D 536 " ideal model delta sigma weight residual 116.30 134.40 -18.10 3.50e+00 8.16e-02 2.67e+01 angle pdb=" CA LEU B 536 " pdb=" CB LEU B 536 " pdb=" CG LEU B 536 " ideal model delta sigma weight residual 116.30 134.26 -17.96 3.50e+00 8.16e-02 2.63e+01 angle pdb=" C GLU B 403 " pdb=" N ILE B 404 " pdb=" CA ILE B 404 " ideal model delta sigma weight residual 120.24 123.47 -3.23 6.30e-01 2.52e+00 2.63e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10523 18.00 - 35.99: 1041 35.99 - 53.99: 188 53.99 - 71.98: 44 71.98 - 89.98: 16 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ASP B 406 " pdb=" C ASP B 406 " pdb=" N ILE B 407 " pdb=" CA ILE B 407 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP C 406 " pdb=" C ASP C 406 " pdb=" N ILE C 407 " pdb=" CA ILE C 407 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASP D 406 " pdb=" C ASP D 406 " pdb=" N ILE D 407 " pdb=" CA ILE D 407 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2915 0.117 - 0.234: 140 0.234 - 0.350: 11 0.350 - 0.467: 2 0.467 - 0.584: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL A 585 " pdb=" CA VAL A 585 " pdb=" CG1 VAL A 585 " pdb=" CG2 VAL A 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CB VAL D 585 " pdb=" CA VAL D 585 " pdb=" CG1 VAL D 585 " pdb=" CG2 VAL D 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 487 " 0.018 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE A 487 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 487 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 487 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 487 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 487 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 574 " 0.020 2.00e-02 2.50e+03 1.83e-02 5.86e+00 pdb=" CG PHE B 574 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 574 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 574 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 574 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 574 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 311 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 312 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.035 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6276 2.85 - 3.36: 17954 3.36 - 3.88: 32373 3.88 - 4.39: 37671 4.39 - 4.90: 64067 Nonbonded interactions: 158341 Sorted by model distance: nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.340 3.040 nonbonded pdb=" O MET C 577 " pdb=" OG1 THR C 581 " model vdw 2.342 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.342 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.351 3.040 nonbonded pdb=" O MET A 577 " pdb=" OG1 THR A 581 " model vdw 2.361 3.040 ... (remaining 158336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.160 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.005 0.065 19860 Z= 0.340 Angle : 1.093 18.443 26964 Z= 0.556 Chirality : 0.061 0.584 3072 Planarity : 0.008 0.060 3416 Dihedral : 14.919 89.976 7236 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.09 % 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: -3.33 (0.13), residues: 2408 helix: -2.38 (0.10), residues: 1420 sheet: -0.78 (0.48), residues: 92 loop : -1.75 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 268 HIS 0.005 0.001 HIS C 201 PHE 0.055 0.003 PHE A 487 TYR 0.017 0.002 TYR B 547 ARG 0.005 0.001 ARG A 385 *********************** 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 340 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 2.335 Fit side-chains REVERT: A 177 GLU cc_start: 0.7814 (mp0) cc_final: 0.7501 (pm20) REVERT: A 255 MET cc_start: 0.8830 (tpp) cc_final: 0.8623 (tpp) REVERT: A 302 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7474 (ttm-80) REVERT: A 481 MET cc_start: 0.8743 (tpt) cc_final: 0.8306 (tpt) REVERT: B 55 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 177 GLU cc_start: 0.7800 (mp0) cc_final: 0.7535 (pm20) REVERT: B 302 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7467 (ttm-80) REVERT: B 440 MET cc_start: 0.7935 (ttp) cc_final: 0.7628 (ttp) REVERT: B 481 MET cc_start: 0.8731 (tpt) cc_final: 0.8273 (tpt) REVERT: C 177 GLU cc_start: 0.7822 (mp0) cc_final: 0.7514 (pm20) REVERT: C 302 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7479 (ttm-80) REVERT: D 177 GLU cc_start: 0.7801 (mp0) cc_final: 0.7532 (pm20) REVERT: D 302 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7470 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2876 time to fit residues: 153.6503 Evaluate side-chains 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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: 0.7980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 261 GLN A 513 GLN A 635 ASN B 208 ASN B 261 GLN B 513 GLN B 635 ASN C 197 ASN C 208 ASN C 214 GLN C 261 GLN C 513 GLN C 635 ASN D 208 ASN D 261 GLN D 513 GLN D 635 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19860 Z= 0.241 Angle : 0.636 12.312 26964 Z= 0.315 Chirality : 0.042 0.215 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.731 22.408 2644 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.28 % Favored : 97.55 % Rotamer: Outliers : 0.72 % Allowed : 9.54 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2408 helix: -0.31 (0.13), residues: 1464 sheet: -0.73 (0.49), residues: 92 loop : -1.16 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 583 HIS 0.006 0.001 HIS D 426 PHE 0.019 0.001 PHE B 574 TYR 0.010 0.001 TYR A 555 ARG 0.002 0.000 ARG B 632 *********************** 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 259 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.451 Fit side-chains REVERT: A 177 GLU cc_start: 0.7876 (mp0) cc_final: 0.7664 (pm20) REVERT: B 55 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 177 GLU cc_start: 0.7886 (mp0) cc_final: 0.7668 (pm20) REVERT: C 637 HIS cc_start: 0.7369 (p-80) cc_final: 0.7129 (p90) REVERT: D 55 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 637 HIS cc_start: 0.7372 (p-80) cc_final: 0.7122 (p90) outliers start: 15 outliers final: 12 residues processed: 253 average time/residue: 0.2974 time to fit residues: 120.8846 Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN B 310 GLN C 252 ASN D 252 ASN D 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1958 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= 0.203 Angle : 0.574 10.322 26964 Z= 0.285 Chirality : 0.041 0.205 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.451 20.647 2644 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.41 % Favored : 97.43 % Rotamer: Outliers : 0.91 % Allowed : 12.21 % Favored : 86.88 % 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: -0.14 (0.17), residues: 2408 helix: 0.49 (0.13), residues: 1468 sheet: -0.69 (0.47), residues: 92 loop : -0.92 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.004 0.001 HIS B 426 PHE 0.015 0.001 PHE C 574 TYR 0.010 0.001 TYR B 555 ARG 0.002 0.000 ARG B 632 *********************** 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 261 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 2.273 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 258 average time/residue: 0.2790 time to fit residues: 115.1992 Evaluate side-chains 234 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19860 Z= 0.234 Angle : 0.575 9.798 26964 Z= 0.286 Chirality : 0.041 0.209 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.369 20.167 2644 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.59 % Rotamer: Outliers : 1.24 % Allowed : 13.65 % Favored : 85.11 % 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: 0.30 (0.17), residues: 2408 helix: 0.86 (0.14), residues: 1464 sheet: -0.89 (0.44), residues: 92 loop : -0.71 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.004 0.001 HIS B 637 PHE 0.019 0.001 PHE C 574 TYR 0.010 0.001 TYR B 555 ARG 0.002 0.000 ARG B 632 *********************** 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 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 2.210 Fit side-chains REVERT: D 487 PHE cc_start: 0.8108 (m-10) cc_final: 0.7673 (m-10) outliers start: 26 outliers final: 16 residues processed: 239 average time/residue: 0.2868 time to fit residues: 110.3060 Evaluate side-chains 227 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19860 Z= 0.240 Angle : 0.571 9.515 26964 Z= 0.284 Chirality : 0.041 0.204 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.338 20.587 2644 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.86 % Allowed : 14.41 % Favored : 83.73 % 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: 0.57 (0.17), residues: 2408 helix: 1.14 (0.14), residues: 1444 sheet: -1.03 (0.43), residues: 92 loop : -0.66 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 593 HIS 0.003 0.001 HIS B 637 PHE 0.020 0.001 PHE C 574 TYR 0.008 0.001 TYR C 89 ARG 0.003 0.000 ARG B 632 *********************** 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 267 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.220 Fit side-chains REVERT: A 637 HIS cc_start: 0.7367 (p-80) cc_final: 0.7098 (p90) REVERT: B 302 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7631 (ttm-80) REVERT: B 554 MET cc_start: 0.8415 (tpt) cc_final: 0.8170 (tpt) REVERT: D 302 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7635 (ttm-80) REVERT: D 522 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8177 (mp0) outliers start: 39 outliers final: 21 residues processed: 260 average time/residue: 0.2958 time to fit residues: 121.9635 Evaluate side-chains 236 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 chunk 192 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19860 Z= 0.145 Angle : 0.538 11.377 26964 Z= 0.264 Chirality : 0.039 0.184 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.121 19.266 2644 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.95 % Allowed : 15.94 % Favored : 83.11 % 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: 0.90 (0.17), residues: 2408 helix: 1.44 (0.14), residues: 1444 sheet: -0.92 (0.44), residues: 92 loop : -0.60 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.002 0.000 HIS B 637 PHE 0.030 0.001 PHE C 574 TYR 0.009 0.001 TYR B 555 ARG 0.002 0.000 ARG B 632 *********************** 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 261 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 2.013 Fit side-chains REVERT: A 522 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: A 596 GLN cc_start: 0.8325 (pt0) cc_final: 0.8109 (pt0) REVERT: B 302 ARG cc_start: 0.8003 (mtp-110) cc_final: 0.7619 (ttm-80) REVERT: B 481 MET cc_start: 0.8894 (tpp) cc_final: 0.8678 (tpt) REVERT: B 554 MET cc_start: 0.8457 (tpt) cc_final: 0.8233 (tpt) REVERT: C 302 ARG cc_start: 0.8021 (mtp-110) cc_final: 0.7629 (ttm-80) REVERT: C 596 GLN cc_start: 0.8319 (pt0) cc_final: 0.8113 (pt0) REVERT: D 302 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7625 (ttm-80) REVERT: D 596 GLN cc_start: 0.8332 (pt0) cc_final: 0.8091 (pt0) outliers start: 20 outliers final: 16 residues processed: 255 average time/residue: 0.3064 time to fit residues: 122.4969 Evaluate side-chains 241 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19860 Z= 0.154 Angle : 0.534 10.310 26964 Z= 0.263 Chirality : 0.039 0.178 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.050 18.594 2644 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.86 % Allowed : 16.75 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2408 helix: 1.63 (0.14), residues: 1444 sheet: -0.73 (0.46), residues: 92 loop : -0.50 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.002 0.000 HIS B 637 PHE 0.026 0.001 PHE B 574 TYR 0.019 0.001 TYR D 547 ARG 0.002 0.000 ARG C 632 *********************** 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 249 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 4.307 Fit side-chains REVERT: A 596 GLN cc_start: 0.8311 (pt0) cc_final: 0.8098 (pt0) REVERT: B 481 MET cc_start: 0.8897 (tpp) cc_final: 0.8661 (tpt) REVERT: C 596 GLN cc_start: 0.8317 (pt0) cc_final: 0.8100 (pt0) REVERT: D 302 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7631 (ttm-80) REVERT: D 522 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (mp0) outliers start: 18 outliers final: 12 residues processed: 242 average time/residue: 0.2877 time to fit residues: 111.4984 Evaluate side-chains 235 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19860 Z= 0.291 Angle : 0.608 11.798 26964 Z= 0.298 Chirality : 0.042 0.201 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.252 21.665 2644 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.29 % Allowed : 16.51 % Favored : 82.20 % 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: 1.50 (0.14), residues: 1456 sheet: -0.82 (0.46), residues: 92 loop : -0.56 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 583 HIS 0.004 0.001 HIS B 637 PHE 0.016 0.001 PHE D 115 TYR 0.019 0.001 TYR C 547 ARG 0.003 0.000 ARG C 589 *********************** 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 250 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 2.613 Fit side-chains REVERT: B 481 MET cc_start: 0.8879 (tpp) cc_final: 0.8662 (tpt) REVERT: C 481 MET cc_start: 0.8935 (tpp) cc_final: 0.8709 (tpt) REVERT: D 302 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7699 (ttm-80) REVERT: D 522 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8231 (mp0) outliers start: 27 outliers final: 21 residues processed: 242 average time/residue: 0.3031 time to fit residues: 116.6190 Evaluate side-chains 238 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2822 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= 0.261 Angle : 0.600 10.970 26964 Z= 0.295 Chirality : 0.041 0.197 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.260 21.449 2644 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.38 % Allowed : 16.56 % Favored : 82.06 % 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 (0.17), residues: 2408 helix: 1.51 (0.14), residues: 1456 sheet: -0.80 (0.46), residues: 92 loop : -0.54 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 583 HIS 0.004 0.001 HIS B 637 PHE 0.030 0.001 PHE B 574 TYR 0.019 0.001 TYR A 547 ARG 0.003 0.000 ARG C 632 *********************** 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 242 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 2.196 Fit side-chains REVERT: A 522 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: B 481 MET cc_start: 0.8875 (tpp) cc_final: 0.8585 (tpt) REVERT: C 481 MET cc_start: 0.8929 (tpp) cc_final: 0.8699 (tpt) REVERT: D 302 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7734 (ttm-80) REVERT: D 522 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8226 (mp0) outliers start: 29 outliers final: 27 residues processed: 234 average time/residue: 0.2931 time to fit residues: 108.7862 Evaluate side-chains 240 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 0.0070 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 596 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19860 Z= 0.166 Angle : 0.553 9.342 26964 Z= 0.273 Chirality : 0.039 0.180 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.070 18.776 2644 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.05 % Allowed : 17.03 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2408 helix: 1.70 (0.14), residues: 1452 sheet: -0.70 (0.46), residues: 92 loop : -0.51 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.003 0.000 HIS B 637 PHE 0.023 0.001 PHE A 574 TYR 0.017 0.001 TYR A 547 ARG 0.002 0.000 ARG D 632 ********************** 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 244 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 2.311 Fit side-chains REVERT: B 481 MET cc_start: 0.8895 (tpp) cc_final: 0.8656 (tpt) REVERT: B 578 MET cc_start: 0.7831 (mtt) cc_final: 0.7527 (mtt) REVERT: C 481 MET cc_start: 0.8919 (tpp) cc_final: 0.8644 (tpt) REVERT: C 578 MET cc_start: 0.7784 (mtt) cc_final: 0.7503 (mtt) REVERT: D 522 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8160 (mp0) outliers start: 22 outliers final: 15 residues processed: 238 average time/residue: 0.2765 time to fit residues: 105.9382 Evaluate side-chains 232 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 522 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096975 restraints weight = 28181.166| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.57 r_work: 0.2826 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19860 Z= 0.161 Angle : 0.548 9.415 26964 Z= 0.270 Chirality : 0.039 0.176 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.020 19.097 2644 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.95 % Allowed : 17.32 % Favored : 81.73 % 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: 1.35 (0.18), residues: 2408 helix: 1.82 (0.14), residues: 1452 sheet: -0.70 (0.46), residues: 92 loop : -0.49 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 593 HIS 0.002 0.000 HIS B 637 PHE 0.020 0.001 PHE C 115 TYR 0.020 0.001 TYR C 547 ARG 0.002 0.000 ARG A 632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3826.85 seconds wall clock time: 71 minutes 6.47 seconds (4266.47 seconds total)