Starting phenix.real_space_refine on Sat Mar 16 18:55:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nmn_12466/03_2024/7nmn_12466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nmn_12466/03_2024/7nmn_12466.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/7nmn_12466/03_2024/7nmn_12466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nmn_12466/03_2024/7nmn_12466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nmn_12466/03_2024/7nmn_12466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nmn_12466/03_2024/7nmn_12466.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 128 5.16 5 C 10000 2.51 5 N 2608 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 559": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C GLU 696": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D GLU 696": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15436 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3859 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain breaks: 1 Chain: "B" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3859 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain breaks: 1 Chain: "C" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3859 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain breaks: 1 Chain: "D" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3859 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain breaks: 1 Time building chain proxies: 8.12, per 1000 atoms: 0.53 Number of scatterers: 15436 At special positions: 0 Unit cell: (128.905, 128.905, 120.015, 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 128 16.00 O 2700 8.00 N 2608 7.00 C 10000 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: 5.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 69.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.069A pdb=" N GLY A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 removed outlier: 3.575A pdb=" N PHE A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 4.066A pdb=" N THR A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N ILE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.696A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 444 Proline residue: A 441 - end of helix removed outlier: 3.658A pdb=" N GLN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.571A pdb=" N TYR A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS A 589 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS A 663 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 237 through 252 removed outlier: 4.068A pdb=" N GLY B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 removed outlier: 3.574A pdb=" N PHE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Proline residue: B 282 - end of helix removed outlier: 4.066A pdb=" N THR B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.655A pdb=" N ILE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.695A pdb=" N LEU B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 444 Proline residue: B 441 - end of helix removed outlier: 3.657A pdb=" N GLN B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 461 through 478 removed outlier: 3.571A pdb=" N TYR B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 542 " --> pdb=" O TYR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 592 removed outlier: 3.580A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS B 589 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS B 663 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 237 through 252 removed outlier: 4.070A pdb=" N GLY C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 removed outlier: 3.574A pdb=" N PHE C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Proline residue: C 282 - end of helix removed outlier: 4.066A pdb=" N THR C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.656A pdb=" N ILE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 340 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.695A pdb=" N LEU C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 444 Proline residue: C 441 - end of helix removed outlier: 3.658A pdb=" N GLN C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.572A pdb=" N TYR C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG C 526 " --> pdb=" O ASP C 522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS C 542 " --> pdb=" O TYR C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 558 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS C 589 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 660 through 665 removed outlier: 3.522A pdb=" N CYS C 663 " --> pdb=" O GLY C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 237 through 252 removed outlier: 4.069A pdb=" N GLY D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 removed outlier: 3.575A pdb=" N PHE D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Proline residue: D 282 - end of helix removed outlier: 4.066A pdb=" N THR D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 removed outlier: 3.655A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 388 Processing helix chain 'D' and resid 391 through 407 removed outlier: 3.696A pdb=" N LEU D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 444 Proline residue: D 441 - end of helix removed outlier: 3.658A pdb=" N GLN D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 461 through 478 removed outlier: 3.572A pdb=" N TYR D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG D 526 " --> pdb=" O ASP D 522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS D 542 " --> pdb=" O TYR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 558 Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 574 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS D 589 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS D 663 " --> pdb=" O GLY D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'D' and resid 697 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 617 Processing sheet with id=AA2, first strand: chain 'A' and resid 651 through 654 removed outlier: 3.609A pdb=" N SER A 673 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 613 through 617 Processing sheet with id=AA4, first strand: chain 'B' and resid 651 through 654 removed outlier: 3.610A pdb=" N SER B 673 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 613 through 617 Processing sheet with id=AA6, first strand: chain 'C' and resid 651 through 654 removed outlier: 3.610A pdb=" N SER C 673 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 617 Processing sheet with id=AA8, first strand: chain 'D' and resid 651 through 654 removed outlier: 3.609A pdb=" N SER D 673 " --> pdb=" O LEU D 644 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 6.02 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: 3081 1.33 - 1.45: 3873 1.45 - 1.57: 8634 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 15812 Sorted by residual: bond pdb=" N LEU B 665 " pdb=" CA LEU B 665 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" N LEU D 665 " pdb=" CA LEU D 665 " ideal model delta sigma weight residual 1.456 1.502 -0.047 1.35e-02 5.49e+03 1.20e+01 bond pdb=" N LEU A 665 " pdb=" CA LEU A 665 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.35e-02 5.49e+03 1.19e+01 bond pdb=" N LEU C 665 " pdb=" CA LEU C 665 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.35e-02 5.49e+03 1.16e+01 bond pdb=" N ILE B 399 " pdb=" CA ILE B 399 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 9.84e+00 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.77: 328 105.77 - 112.94: 8103 112.94 - 120.12: 6692 120.12 - 127.29: 6077 127.29 - 134.46: 156 Bond angle restraints: 21356 Sorted by residual: angle pdb=" C ASN D 459 " pdb=" CA ASN D 459 " pdb=" CB ASN D 459 " ideal model delta sigma weight residual 110.19 120.06 -9.87 1.62e+00 3.81e-01 3.71e+01 angle pdb=" C ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta sigma weight residual 110.19 120.04 -9.85 1.62e+00 3.81e-01 3.70e+01 angle pdb=" C ASN C 459 " pdb=" CA ASN C 459 " pdb=" CB ASN C 459 " ideal model delta sigma weight residual 110.19 120.03 -9.84 1.62e+00 3.81e-01 3.69e+01 angle pdb=" C ASN B 459 " pdb=" CA ASN B 459 " pdb=" CB ASN B 459 " ideal model delta sigma weight residual 110.19 120.01 -9.82 1.62e+00 3.81e-01 3.67e+01 angle pdb=" CA HIS D 400 " pdb=" C HIS D 400 " pdb=" O HIS D 400 " ideal model delta sigma weight residual 120.82 115.77 5.05 1.05e+00 9.07e-01 2.31e+01 ... (remaining 21351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 8372 16.99 - 33.98: 836 33.98 - 50.97: 156 50.97 - 67.96: 44 67.96 - 84.95: 8 Dihedral angle restraints: 9416 sinusoidal: 3912 harmonic: 5504 Sorted by residual: dihedral pdb=" C ASN D 459 " pdb=" N ASN D 459 " pdb=" CA ASN D 459 " pdb=" CB ASN D 459 " ideal model delta harmonic sigma weight residual -122.60 -136.06 13.46 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C ASN A 459 " pdb=" N ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta harmonic sigma weight residual -122.60 -136.02 13.42 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" C ASN B 459 " pdb=" N ASN B 459 " pdb=" CA ASN B 459 " pdb=" CB ASN B 459 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 9413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1591 0.077 - 0.153: 605 0.153 - 0.230: 120 0.230 - 0.307: 8 0.307 - 0.384: 4 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ASN D 459 " pdb=" N ASN D 459 " pdb=" C ASN D 459 " pdb=" CB ASN D 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ASN A 459 " pdb=" N ASN A 459 " pdb=" C ASN A 459 " pdb=" CB ASN A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN B 459 " pdb=" N ASN B 459 " pdb=" C ASN B 459 " pdb=" CB ASN B 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 2325 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 397 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C ARG D 397 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG D 397 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR D 398 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 397 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ARG A 397 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 397 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 397 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C ARG B 397 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG B 397 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 398 " -0.018 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5560 2.87 - 3.38: 14687 3.38 - 3.88: 24227 3.88 - 4.39: 26319 4.39 - 4.90: 46009 Nonbonded interactions: 116802 Sorted by model distance: nonbonded pdb=" N ASP A 326 " pdb=" OD1 ASP A 326 " model vdw 2.361 2.520 nonbonded pdb=" N ASP C 326 " pdb=" OD1 ASP C 326 " model vdw 2.361 2.520 nonbonded pdb=" N ASP B 326 " pdb=" OD1 ASP B 326 " model vdw 2.362 2.520 nonbonded pdb=" N ASP D 326 " pdb=" OD1 ASP D 326 " model vdw 2.362 2.520 nonbonded pdb=" O ASN A 459 " pdb=" OD1 ASN A 459 " model vdw 2.367 3.040 ... (remaining 116797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 6.380 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 40.910 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.010 0.070 15812 Z= 0.629 Angle : 1.163 9.867 21356 Z= 0.816 Chirality : 0.079 0.384 2328 Planarity : 0.008 0.075 2684 Dihedral : 14.026 84.953 5864 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.88 % Allowed : 12.53 % Favored : 86.59 % Cbeta Deviations : 0.23 % 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: -1.43 (0.18), residues: 1860 helix: -0.35 (0.14), residues: 1176 sheet: -1.13 (0.35), residues: 132 loop : -1.97 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 451 HIS 0.006 0.002 HIS B 407 PHE 0.020 0.002 PHE C 253 TYR 0.016 0.002 TYR D 556 ARG 0.012 0.001 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 291 time to evaluate : 1.888 Fit side-chains REVERT: A 433 ASP cc_start: 0.7950 (t0) cc_final: 0.7725 (t0) REVERT: A 679 TYR cc_start: 0.8133 (m-80) cc_final: 0.7878 (m-80) REVERT: A 696 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: B 433 ASP cc_start: 0.7980 (t0) cc_final: 0.7750 (t0) REVERT: B 460 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: B 696 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: C 433 ASP cc_start: 0.8020 (t0) cc_final: 0.7787 (t0) REVERT: C 460 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (m-40) REVERT: C 696 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: D 433 ASP cc_start: 0.8007 (t0) cc_final: 0.7769 (t0) REVERT: D 460 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (m-40) outliers start: 15 outliers final: 8 residues processed: 306 average time/residue: 0.2861 time to fit residues: 127.2744 Evaluate side-chains 222 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 480 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 444 GLN A 455 ASN A 459 ASN A 460 ASN A 519 GLN A 537 GLN A 542 HIS A 586 ASN A 691 ASN B 245 GLN B 444 GLN B 455 ASN B 459 ASN B 519 GLN B 542 HIS B 586 ASN B 603 ASN C 245 GLN C 444 GLN C 455 ASN C 459 ASN C 519 GLN C 542 HIS C 586 ASN C 603 ASN D 245 GLN D 444 GLN D 455 ASN D 459 ASN D 519 GLN D 542 HIS D 586 ASN D 603 ASN D 691 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15812 Z= 0.245 Angle : 0.586 6.188 21356 Z= 0.308 Chirality : 0.040 0.122 2328 Planarity : 0.005 0.050 2684 Dihedral : 6.353 78.612 2111 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 14.59 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1860 helix: 1.19 (0.15), residues: 1184 sheet: -0.80 (0.38), residues: 132 loop : -1.62 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 462 HIS 0.003 0.001 HIS A 513 PHE 0.011 0.002 PHE D 659 TYR 0.010 0.001 TYR A 532 ARG 0.003 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 242 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8753 (tp) cc_final: 0.8553 (tp) REVERT: B 222 MET cc_start: 0.6776 (mtt) cc_final: 0.6317 (mtm) REVERT: B 233 ARG cc_start: 0.7947 (tmm-80) cc_final: 0.7662 (ttt180) REVERT: C 233 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7712 (ttt180) REVERT: D 222 MET cc_start: 0.6763 (mtt) cc_final: 0.6326 (mtm) REVERT: D 233 ARG cc_start: 0.7979 (tmm-80) cc_final: 0.7674 (ttt180) REVERT: D 270 MET cc_start: 0.8271 (mmm) cc_final: 0.8032 (mmm) REVERT: D 402 TRP cc_start: 0.7601 (m100) cc_final: 0.7396 (m100) outliers start: 53 outliers final: 26 residues processed: 287 average time/residue: 0.2856 time to fit residues: 118.0645 Evaluate side-chains 243 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 134 optimal weight: 5.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15812 Z= 0.206 Angle : 0.535 8.186 21356 Z= 0.276 Chirality : 0.039 0.121 2328 Planarity : 0.004 0.044 2684 Dihedral : 4.814 50.635 2088 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 16.94 % Favored : 80.29 % 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: 0.98 (0.20), residues: 1860 helix: 1.67 (0.16), residues: 1188 sheet: -0.51 (0.39), residues: 132 loop : -1.35 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 451 HIS 0.002 0.001 HIS B 553 PHE 0.021 0.001 PHE B 343 TYR 0.010 0.001 TYR B 507 ARG 0.003 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8718 (tp) cc_final: 0.8506 (tp) REVERT: B 273 LEU cc_start: 0.8719 (tp) cc_final: 0.8486 (tp) REVERT: B 477 MET cc_start: 0.8252 (ttp) cc_final: 0.8009 (ttp) REVERT: C 233 ARG cc_start: 0.8144 (tmm-80) cc_final: 0.7872 (ttt180) REVERT: D 222 MET cc_start: 0.6861 (mtt) cc_final: 0.6395 (mtm) outliers start: 47 outliers final: 31 residues processed: 269 average time/residue: 0.2586 time to fit residues: 104.4051 Evaluate side-chains 259 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 0.0470 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15812 Z= 0.199 Angle : 0.509 6.660 21356 Z= 0.265 Chirality : 0.039 0.120 2328 Planarity : 0.004 0.043 2684 Dihedral : 4.719 52.611 2088 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.00 % Allowed : 18.53 % Favored : 77.47 % 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: 1.18 (0.20), residues: 1860 helix: 1.78 (0.16), residues: 1188 sheet: -0.22 (0.42), residues: 108 loop : -1.20 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 451 HIS 0.002 0.001 HIS B 553 PHE 0.009 0.001 PHE A 659 TYR 0.010 0.001 TYR C 468 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 ARG cc_start: 0.8179 (tmm-80) cc_final: 0.7902 (ttt180) REVERT: D 233 ARG cc_start: 0.8178 (tmm-80) cc_final: 0.7902 (ttt180) outliers start: 68 outliers final: 53 residues processed: 281 average time/residue: 0.2690 time to fit residues: 111.6026 Evaluate side-chains 284 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN D 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15812 Z= 0.327 Angle : 0.586 8.648 21356 Z= 0.307 Chirality : 0.041 0.131 2328 Planarity : 0.004 0.040 2684 Dihedral : 4.914 52.065 2088 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.88 % Allowed : 19.65 % Favored : 76.47 % 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: 0.93 (0.20), residues: 1860 helix: 1.63 (0.16), residues: 1188 sheet: -0.53 (0.39), residues: 132 loop : -1.37 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 451 HIS 0.003 0.001 HIS B 257 PHE 0.024 0.002 PHE B 343 TYR 0.011 0.002 TYR C 507 ARG 0.006 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 232 time to evaluate : 2.129 Fit side-chains REVERT: A 332 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7853 (ptm-80) REVERT: B 233 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7812 (ttt180) REVERT: C 233 ARG cc_start: 0.8114 (tmm-80) cc_final: 0.7805 (ttt180) REVERT: D 233 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7828 (ttt180) outliers start: 66 outliers final: 51 residues processed: 275 average time/residue: 0.2528 time to fit residues: 103.5841 Evaluate side-chains 274 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 223 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15812 Z= 0.429 Angle : 0.643 5.901 21356 Z= 0.340 Chirality : 0.043 0.131 2328 Planarity : 0.005 0.039 2684 Dihedral : 5.154 51.624 2088 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.65 % Allowed : 19.29 % Favored : 76.06 % 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: 0.56 (0.20), residues: 1860 helix: 1.30 (0.15), residues: 1188 sheet: -0.65 (0.40), residues: 132 loop : -1.43 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 451 HIS 0.004 0.001 HIS C 257 PHE 0.013 0.002 PHE A 585 TYR 0.015 0.002 TYR C 507 ARG 0.005 0.001 ARG C 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 237 time to evaluate : 1.966 Fit side-chains REVERT: A 273 LEU cc_start: 0.8719 (tp) cc_final: 0.8512 (tp) REVERT: B 233 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7968 (ttp80) REVERT: C 274 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7711 (tpt) outliers start: 79 outliers final: 63 residues processed: 292 average time/residue: 0.2721 time to fit residues: 116.6402 Evaluate side-chains 293 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 229 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 534 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 534 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN C 534 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN D 534 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15812 Z= 0.126 Angle : 0.475 6.668 21356 Z= 0.248 Chirality : 0.038 0.124 2328 Planarity : 0.004 0.041 2684 Dihedral : 4.588 52.434 2088 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.53 % Allowed : 19.94 % Favored : 76.53 % 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: 1.49 (0.20), residues: 1860 helix: 1.99 (0.16), residues: 1168 sheet: 0.10 (0.47), residues: 88 loop : -0.90 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 451 HIS 0.003 0.001 HIS C 553 PHE 0.007 0.001 PHE A 659 TYR 0.021 0.001 TYR C 507 ARG 0.007 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 1.569 Fit side-chains REVERT: A 230 PHE cc_start: 0.7480 (t80) cc_final: 0.7271 (t80) REVERT: A 273 LEU cc_start: 0.8666 (tp) cc_final: 0.8445 (tp) REVERT: A 332 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7737 (ptm-80) REVERT: A 433 ASP cc_start: 0.8213 (t0) cc_final: 0.7961 (t70) REVERT: A 510 PHE cc_start: 0.8799 (t80) cc_final: 0.8520 (t80) REVERT: A 699 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7634 (mmm) REVERT: B 510 PHE cc_start: 0.8859 (t80) cc_final: 0.8597 (t80) REVERT: C 433 ASP cc_start: 0.8056 (t0) cc_final: 0.7846 (t70) REVERT: C 480 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8572 (pt) REVERT: C 699 MET cc_start: 0.8132 (mmt) cc_final: 0.7930 (mmt) REVERT: D 273 LEU cc_start: 0.8629 (tp) cc_final: 0.8389 (tp) REVERT: D 433 ASP cc_start: 0.8275 (t0) cc_final: 0.8035 (t70) outliers start: 60 outliers final: 44 residues processed: 298 average time/residue: 0.2736 time to fit residues: 120.1490 Evaluate side-chains 286 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 534 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN D 534 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15812 Z= 0.121 Angle : 0.481 9.230 21356 Z= 0.245 Chirality : 0.038 0.118 2328 Planarity : 0.004 0.042 2684 Dihedral : 4.415 51.701 2088 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.53 % Allowed : 20.88 % Favored : 76.59 % 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: 1.68 (0.20), residues: 1860 helix: 2.08 (0.16), residues: 1172 sheet: -0.08 (0.43), residues: 108 loop : -0.66 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 451 HIS 0.003 0.001 HIS C 553 PHE 0.007 0.001 PHE D 659 TYR 0.016 0.001 TYR A 507 ARG 0.006 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 1.749 Fit side-chains REVERT: A 273 LEU cc_start: 0.8674 (tp) cc_final: 0.8422 (tp) REVERT: A 332 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7773 (ptm-80) REVERT: A 392 LEU cc_start: 0.8534 (tp) cc_final: 0.8197 (mt) REVERT: A 410 TYR cc_start: 0.8039 (m-80) cc_final: 0.7639 (m-80) REVERT: A 510 PHE cc_start: 0.8849 (t80) cc_final: 0.8554 (t80) REVERT: B 392 LEU cc_start: 0.8521 (tp) cc_final: 0.8215 (mt) REVERT: B 410 TYR cc_start: 0.8076 (m-80) cc_final: 0.7743 (m-80) REVERT: B 507 TYR cc_start: 0.8770 (t80) cc_final: 0.8475 (t80) REVERT: B 510 PHE cc_start: 0.8804 (t80) cc_final: 0.8524 (t80) REVERT: C 392 LEU cc_start: 0.8548 (tp) cc_final: 0.8228 (mt) REVERT: C 410 TYR cc_start: 0.8080 (m-80) cc_final: 0.7681 (m-80) REVERT: C 433 ASP cc_start: 0.8015 (t0) cc_final: 0.7768 (t70) REVERT: C 480 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (pt) REVERT: C 510 PHE cc_start: 0.8874 (t80) cc_final: 0.8626 (t80) REVERT: D 273 LEU cc_start: 0.8642 (tp) cc_final: 0.8417 (tp) REVERT: D 392 LEU cc_start: 0.8479 (tp) cc_final: 0.8185 (mt) REVERT: D 410 TYR cc_start: 0.8089 (m-80) cc_final: 0.7739 (m-80) REVERT: D 510 PHE cc_start: 0.8850 (t80) cc_final: 0.8466 (t80) outliers start: 43 outliers final: 35 residues processed: 279 average time/residue: 0.2571 time to fit residues: 107.3613 Evaluate side-chains 283 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15812 Z= 0.225 Angle : 0.534 6.953 21356 Z= 0.275 Chirality : 0.039 0.121 2328 Planarity : 0.004 0.041 2684 Dihedral : 4.560 51.008 2088 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.41 % Allowed : 21.29 % Favored : 76.29 % 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: 1.63 (0.20), residues: 1860 helix: 2.00 (0.16), residues: 1172 sheet: -0.08 (0.43), residues: 108 loop : -0.59 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 451 HIS 0.002 0.001 HIS D 257 PHE 0.012 0.001 PHE A 510 TYR 0.009 0.001 TYR A 532 ARG 0.006 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 1.774 Fit side-chains REVERT: A 273 LEU cc_start: 0.8664 (tp) cc_final: 0.8219 (tt) REVERT: A 332 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7430 (ptm-80) REVERT: B 410 TYR cc_start: 0.8216 (m-80) cc_final: 0.7876 (m-80) REVERT: C 222 MET cc_start: 0.6971 (mtt) cc_final: 0.6353 (mtm) REVERT: C 480 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8795 (pt) REVERT: D 392 LEU cc_start: 0.8579 (tp) cc_final: 0.8326 (mt) REVERT: D 410 TYR cc_start: 0.8231 (m-80) cc_final: 0.7924 (m-80) outliers start: 41 outliers final: 38 residues processed: 268 average time/residue: 0.2606 time to fit residues: 103.5087 Evaluate side-chains 276 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 0.0070 chunk 115 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 534 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 534 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN C 534 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN D 534 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15812 Z= 0.125 Angle : 0.488 7.013 21356 Z= 0.248 Chirality : 0.038 0.130 2328 Planarity : 0.004 0.043 2684 Dihedral : 4.391 50.980 2088 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.41 % Allowed : 21.24 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1860 helix: 2.14 (0.15), residues: 1172 sheet: 0.14 (0.44), residues: 108 loop : -0.41 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 451 HIS 0.003 0.000 HIS A 553 PHE 0.011 0.001 PHE A 510 TYR 0.010 0.001 TYR A 532 ARG 0.007 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.654 Fit side-chains REVERT: A 273 LEU cc_start: 0.8629 (tp) cc_final: 0.8407 (tp) REVERT: A 332 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7901 (ptm-80) REVERT: A 410 TYR cc_start: 0.7974 (m-80) cc_final: 0.7604 (m-80) REVERT: A 507 TYR cc_start: 0.8911 (t80) cc_final: 0.8645 (t80) REVERT: B 392 LEU cc_start: 0.8491 (tp) cc_final: 0.8194 (mt) REVERT: B 410 TYR cc_start: 0.8010 (m-80) cc_final: 0.7786 (m-80) REVERT: B 510 PHE cc_start: 0.8845 (t80) cc_final: 0.8476 (t80) REVERT: C 392 LEU cc_start: 0.8471 (tp) cc_final: 0.8190 (mt) REVERT: C 410 TYR cc_start: 0.8029 (m-80) cc_final: 0.7670 (m-80) REVERT: C 510 PHE cc_start: 0.8908 (t80) cc_final: 0.8560 (t80) REVERT: D 392 LEU cc_start: 0.8416 (tp) cc_final: 0.8170 (mt) REVERT: D 410 TYR cc_start: 0.8014 (m-80) cc_final: 0.7789 (m-80) REVERT: D 510 PHE cc_start: 0.8819 (t80) cc_final: 0.8447 (t80) outliers start: 41 outliers final: 38 residues processed: 287 average time/residue: 0.2500 time to fit residues: 107.7442 Evaluate side-chains 295 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 534 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN B 534 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN C 534 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN D 534 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130385 restraints weight = 21950.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129003 restraints weight = 15613.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130132 restraints weight = 12379.706| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15812 Z= 0.157 Angle : 0.504 6.648 21356 Z= 0.258 Chirality : 0.039 0.139 2328 Planarity : 0.004 0.041 2684 Dihedral : 4.377 50.522 2088 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.53 % Allowed : 21.35 % Favored : 76.12 % 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: 1.89 (0.20), residues: 1860 helix: 2.07 (0.15), residues: 1184 sheet: 0.21 (0.44), residues: 108 loop : -0.25 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 451 HIS 0.003 0.001 HIS A 553 PHE 0.015 0.001 PHE D 307 TYR 0.009 0.001 TYR A 532 ARG 0.007 0.000 ARG B 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.26 seconds wall clock time: 53 minutes 7.01 seconds (3187.01 seconds total)