Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:02:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/02_2023/6bo8_7120.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 10.76, per 1000 atoms: 0.56 Number of scatterers: 19048 At special positions: 0 Unit cell: (136.22, 136.22, 125.44, 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 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 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: 7.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.686A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.685A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.803A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.013A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.647A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.636A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.531A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 346 Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.190A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.010A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.570A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.527A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.688A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.637A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.547A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.775A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 492 Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 587 Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2532 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: 5.36 Time building geometry restraints manager: 8.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5464 1.33 - 1.45: 3323 1.45 - 1.57: 10433 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" CA VAL C 452 " pdb=" CB VAL C 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.97e+00 bond pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.93e+00 bond pdb=" CA VAL D 452 " pdb=" CB VAL D 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.69e+00 bond pdb=" CA HIS C 265 " pdb=" CB HIS C 265 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" CA VAL B 452 " pdb=" CB VAL B 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.63e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.13: 423 105.13 - 112.51: 10061 112.51 - 119.88: 7131 119.88 - 127.26: 8556 127.26 - 134.63: 269 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N LEU D 352 " pdb=" CA LEU D 352 " pdb=" C LEU D 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU A 352 " pdb=" CA LEU A 352 " pdb=" C LEU A 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU C 352 " pdb=" CA LEU C 352 " pdb=" C LEU C 352 " ideal model delta sigma weight residual 110.91 118.00 -7.09 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.99 -7.08 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.52 -8.73 1.53e+00 4.27e-01 3.26e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 10858 15.42 - 30.85: 657 30.85 - 46.27: 157 46.27 - 61.69: 4 61.69 - 77.11: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta harmonic sigma weight residual -180.00 -149.04 -30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASP D 223 " pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2014 0.051 - 0.103: 827 0.103 - 0.154: 141 0.154 - 0.205: 19 0.205 - 0.256: 11 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP D 223 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG D 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASP C 223 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASP A 223 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 224 " -0.015 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5470 2.81 - 3.33: 19064 3.33 - 3.85: 31397 3.85 - 4.38: 37260 4.38 - 4.90: 60177 Nonbonded interactions: 153368 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.310 2.440 ... (remaining 153363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 3.730 Check model and map are aligned: 0.300 Process input model: 47.770 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 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 : 0.008 0.065 19484 Z= 0.490 Angle : 1.192 18.330 26440 Z= 0.668 Chirality : 0.055 0.256 3012 Planarity : 0.007 0.049 3336 Dihedral : 10.831 77.114 7184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.49 (0.14), residues: 2356 helix: -2.68 (0.10), residues: 1344 sheet: -5.00 (0.44), residues: 56 loop : -3.13 (0.18), residues: 956 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 759 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 0 residues processed: 769 average time/residue: 0.3232 time to fit residues: 366.8775 Evaluate side-chains 430 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 184 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 165 HIS A 206 GLN A 522 HIS B 118 GLN B 165 HIS B 206 GLN B 426 HIS B 546 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 165 HIS C 206 GLN C 265 HIS C 464 ASN C 522 HIS D 118 GLN D 165 HIS D 206 GLN ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 522 HIS D 548 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19484 Z= 0.228 Angle : 0.754 11.997 26440 Z= 0.376 Chirality : 0.043 0.216 3012 Planarity : 0.005 0.045 3336 Dihedral : 5.759 29.453 2596 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.32 % Rotamer Outliers : 3.00 % 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: -2.13 (0.17), residues: 2356 helix: -0.47 (0.13), residues: 1356 sheet: -4.33 (0.50), residues: 56 loop : -2.62 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 502 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 35 residues processed: 544 average time/residue: 0.2869 time to fit residues: 243.4402 Evaluate side-chains 431 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 396 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1699 time to fit residues: 14.2423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 0.3980 chunk 231 optimal weight: 0.0170 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 0.0670 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 267 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 572 ASN D 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19484 Z= 0.211 Angle : 0.722 12.203 26440 Z= 0.354 Chirality : 0.042 0.244 3012 Planarity : 0.004 0.046 3336 Dihedral : 5.328 31.257 2596 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.47 (0.17), residues: 2356 helix: 0.24 (0.14), residues: 1364 sheet: -3.93 (0.52), residues: 56 loop : -2.67 (0.20), residues: 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 460 time to evaluate : 2.076 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 490 average time/residue: 0.2758 time to fit residues: 213.2244 Evaluate side-chains 403 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 376 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1653 time to fit residues: 11.9394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN B 258 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19484 Z= 0.202 Angle : 0.703 13.276 26440 Z= 0.341 Chirality : 0.041 0.200 3012 Planarity : 0.004 0.044 3336 Dihedral : 5.077 28.226 2596 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.42 % Favored : 90.53 % Rotamer Outliers : 2.33 % 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: -1.07 (0.18), residues: 2356 helix: 0.60 (0.14), residues: 1360 sheet: -3.69 (0.53), residues: 56 loop : -2.57 (0.20), residues: 940 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 412 time to evaluate : 2.288 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 440 average time/residue: 0.2733 time to fit residues: 190.9834 Evaluate side-chains 387 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1720 time to fit residues: 10.0024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 267 GLN D 206 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 19484 Z= 0.414 Angle : 0.807 13.032 26440 Z= 0.400 Chirality : 0.046 0.185 3012 Planarity : 0.005 0.050 3336 Dihedral : 5.339 29.466 2596 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer Outliers : 3.73 % 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: -1.28 (0.17), residues: 2356 helix: 0.41 (0.14), residues: 1368 sheet: -3.49 (0.49), residues: 56 loop : -2.65 (0.20), residues: 932 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 390 time to evaluate : 2.308 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 23 residues processed: 439 average time/residue: 0.2986 time to fit residues: 202.4098 Evaluate side-chains 359 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 336 time to evaluate : 2.270 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1728 time to fit residues: 10.6732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 158 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19484 Z= 0.216 Angle : 0.721 11.673 26440 Z= 0.349 Chirality : 0.043 0.229 3012 Planarity : 0.004 0.046 3336 Dihedral : 5.091 28.420 2596 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer Outliers : 2.03 % 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: -0.96 (0.18), residues: 2356 helix: 0.72 (0.14), residues: 1356 sheet: -3.32 (0.49), residues: 56 loop : -2.56 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 378 time to evaluate : 2.260 Fit side-chains outliers start: 42 outliers final: 18 residues processed: 403 average time/residue: 0.2962 time to fit residues: 185.2290 Evaluate side-chains 359 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 341 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1751 time to fit residues: 9.1163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 0.0030 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19484 Z= 0.177 Angle : 0.708 12.508 26440 Z= 0.341 Chirality : 0.042 0.234 3012 Planarity : 0.004 0.036 3336 Dihedral : 4.872 32.810 2596 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.79 (0.18), residues: 2356 helix: 0.88 (0.14), residues: 1356 sheet: -2.87 (0.54), residues: 56 loop : -2.57 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 388 time to evaluate : 2.383 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 403 average time/residue: 0.3072 time to fit residues: 192.7549 Evaluate side-chains 355 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 344 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2387 time to fit residues: 7.5428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19484 Z= 0.189 Angle : 0.707 11.602 26440 Z= 0.340 Chirality : 0.042 0.230 3012 Planarity : 0.004 0.042 3336 Dihedral : 4.815 30.755 2596 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.65 (0.18), residues: 2356 helix: 1.00 (0.14), residues: 1356 sheet: -2.68 (0.56), residues: 56 loop : -2.54 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 356 time to evaluate : 2.388 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 369 average time/residue: 0.3006 time to fit residues: 171.2823 Evaluate side-chains 349 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 339 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1664 time to fit residues: 6.1927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 224 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19484 Z= 0.184 Angle : 0.708 12.091 26440 Z= 0.340 Chirality : 0.042 0.244 3012 Planarity : 0.004 0.038 3336 Dihedral : 4.739 30.608 2596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.18), residues: 2356 helix: 1.09 (0.14), residues: 1352 sheet: -2.49 (0.56), residues: 56 loop : -2.54 (0.20), residues: 948 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 359 time to evaluate : 2.475 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 368 average time/residue: 0.2926 time to fit residues: 169.5175 Evaluate side-chains 351 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 2.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1687 time to fit residues: 4.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 199 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 19484 Z= 0.245 Angle : 0.740 13.348 26440 Z= 0.356 Chirality : 0.044 0.276 3012 Planarity : 0.004 0.040 3336 Dihedral : 4.796 30.065 2596 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.64 (0.18), residues: 2356 helix: 1.05 (0.14), residues: 1352 sheet: -3.32 (0.46), residues: 76 loop : -2.50 (0.20), residues: 928 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 348 time to evaluate : 2.278 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 351 average time/residue: 0.3059 time to fit residues: 168.3120 Evaluate side-chains 345 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1821 time to fit residues: 6.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 52 optimal weight: 0.0670 chunk 187 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 192 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121318 restraints weight = 28617.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124304 restraints weight = 15444.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126220 restraints weight = 10569.492| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19484 Z= 0.222 Angle : 0.737 12.130 26440 Z= 0.352 Chirality : 0.043 0.272 3012 Planarity : 0.004 0.039 3336 Dihedral : 4.789 30.720 2596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.60 (0.18), residues: 2356 helix: 1.05 (0.14), residues: 1356 sheet: -2.29 (0.57), residues: 56 loop : -2.55 (0.20), residues: 944 =============================================================================== Job complete usr+sys time: 4139.59 seconds wall clock time: 75 minutes 34.11 seconds (4534.11 seconds total)