Starting phenix.real_space_refine on Wed Feb 14 17:07:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j60_33735/02_2024/8j60_33735.pdb" } resolution = 3.39 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= 0.042 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 38 5.16 5 C 6264 2.51 5 N 1619 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9757 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3659 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 469} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 218 Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1179 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1167 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 142} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3752 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 484} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 221 Time building chain proxies: 5.82, per 1000 atoms: 0.60 Number of scatterers: 9757 At special positions: 0 Unit cell: (154.16, 82.82, 81.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1836 8.00 N 1619 7.00 C 6264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 320 " distance=2.03 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: 3.92 Conformation dependent library (CDL) restraints added in 2.3 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 37.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 171 through 176 removed outlier: 4.147A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.714A pdb=" N LEU B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 331 through 349 removed outlier: 3.721A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.761A pdb=" N GLU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 434 removed outlier: 3.816A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.323A pdb=" N GLU B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.058A pdb=" N GLU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.607A pdb=" N LYS B 518 " --> pdb=" O LYS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 4.115A pdb=" N ILE B 570 " --> pdb=" O PRO B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.535A pdb=" N LYS B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.623A pdb=" N SER C 13 " --> pdb=" O TRP C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 32 through 54 Processing helix chain 'C' and resid 57 through 75 Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.901A pdb=" N VAL C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 158 Processing helix chain 'D' and resid 13 through 24 removed outlier: 3.548A pdb=" N VAL D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 removed outlier: 3.781A pdb=" N TYR D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 122 through 135 removed outlier: 3.902A pdb=" N VAL D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 158 Processing helix chain 'A' and resid 225 through 241 removed outlier: 3.542A pdb=" N ILE A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.663A pdb=" N ASP A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.633A pdb=" N ASP A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.850A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.661A pdb=" N PHE A 448 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.191A pdb=" N LEU A 497 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 3.805A pdb=" N LYS A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.853A pdb=" N ILE A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 4.033A pdb=" N ARG A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.584A pdb=" N ILE B 78 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 158 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 161 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 97 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 163 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 95 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 91 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.584A pdb=" N ILE B 78 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 158 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 161 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 97 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 163 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 95 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 319 removed outlier: 5.134A pdb=" N SER B 317 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS B 300 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN B 319 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 298 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 435 through 437 removed outlier: 3.852A pdb=" N ASP B 437 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 455 removed outlier: 7.380A pdb=" N ILE B 538 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 532 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN B 540 " --> pdb=" O HIS B 530 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE B 523 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS B 491 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 525 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 464 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ARG B 560 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR B 466 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 586 through 587 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 81 Processing sheet with id=AB2, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.737A pdb=" N LYS A 90 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.654A pdb=" N ILE A 126 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AB6, first strand: chain 'A' and resid 319 through 321 removed outlier: 4.008A pdb=" N GLN A 319 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 298 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 465 through 467 removed outlier: 6.487A pdb=" N THR A 466 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 489 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG A 525 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 491 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A 523 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 530 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 540 " --> pdb=" O HIS A 530 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1140 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: 2.94 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3145 1.35 - 1.47: 2488 1.47 - 1.60: 4266 1.60 - 1.73: 0 1.73 - 1.85: 64 Bond restraints: 9963 Sorted by residual: bond pdb=" CB PRO A 445 " pdb=" CG PRO A 445 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.23e+00 bond pdb=" C TYR B 211 " pdb=" O TYR B 211 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.26e+00 bond pdb=" CA CYS A 320 " pdb=" CB CYS A 320 " ideal model delta sigma weight residual 1.527 1.552 -0.026 1.75e-02 3.27e+03 2.13e+00 bond pdb=" CG LEU D 66 " pdb=" CD2 LEU D 66 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" CB CYS A 320 " pdb=" SG CYS A 320 " ideal model delta sigma weight residual 1.808 1.851 -0.043 3.30e-02 9.18e+02 1.70e+00 ... (remaining 9958 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.33: 183 104.33 - 111.77: 4995 111.77 - 119.22: 3135 119.22 - 126.66: 5101 126.66 - 134.10: 153 Bond angle restraints: 13567 Sorted by residual: angle pdb=" N PRO A 121 " pdb=" CA PRO A 121 " pdb=" CB PRO A 121 " ideal model delta sigma weight residual 103.25 111.34 -8.09 1.05e+00 9.07e-01 5.93e+01 angle pdb=" N PRO B 400 " pdb=" CA PRO B 400 " pdb=" CB PRO B 400 " ideal model delta sigma weight residual 102.60 110.28 -7.68 1.10e+00 8.26e-01 4.88e+01 angle pdb=" N PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 102.33 110.17 -7.84 1.18e+00 7.18e-01 4.41e+01 angle pdb=" N PRO D 102 " pdb=" CA PRO D 102 " pdb=" CB PRO D 102 " ideal model delta sigma weight residual 103.25 110.21 -6.96 1.05e+00 9.07e-01 4.40e+01 angle pdb=" N ILE B 365 " pdb=" CA ILE B 365 " pdb=" C ILE B 365 " ideal model delta sigma weight residual 113.53 107.24 6.29 9.80e-01 1.04e+00 4.12e+01 ... (remaining 13562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5318 17.19 - 34.37: 476 34.37 - 51.56: 93 51.56 - 68.75: 10 68.75 - 85.93: 12 Dihedral angle restraints: 5909 sinusoidal: 2108 harmonic: 3801 Sorted by residual: dihedral pdb=" CA CYS B 295 " pdb=" C CYS B 295 " pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA GLN B 319 " pdb=" C GLN B 319 " pdb=" N CYS B 320 " pdb=" CA CYS B 320 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS A 295 " pdb=" C CYS A 295 " pdb=" N ILE A 296 " pdb=" CA ILE A 296 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1265 0.051 - 0.101: 276 0.101 - 0.152: 60 0.152 - 0.203: 5 0.203 - 0.253: 4 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CA PRO D 102 " pdb=" N PRO D 102 " pdb=" C PRO D 102 " pdb=" CB PRO D 102 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO B 400 " pdb=" N PRO B 400 " pdb=" C PRO B 400 " pdb=" CB PRO B 400 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1607 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 450 " 0.095 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO A 451 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 444 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 445 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 449 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO B 450 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 450 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 450 " 0.037 5.00e-02 4.00e+02 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 144 2.66 - 3.22: 9621 3.22 - 3.78: 14818 3.78 - 4.34: 19794 4.34 - 4.90: 32990 Nonbonded interactions: 77367 Sorted by model distance: nonbonded pdb=" OG1 THR C 87 " pdb=" OG1 THR D 87 " model vdw 2.099 2.440 nonbonded pdb=" O VAL B 249 " pdb=" OG1 THR B 361 " model vdw 2.141 2.440 nonbonded pdb=" NH1 ARG C 94 " pdb=" O ALA D 132 " model vdw 2.150 2.520 nonbonded pdb=" O LYS B 233 " pdb=" OG1 THR B 236 " model vdw 2.175 2.440 nonbonded pdb=" OG SER B 455 " pdb=" OG SER B 459 " model vdw 2.179 2.440 ... (remaining 77362 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' and (resid 60 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 68 or (resid 69 through 70 and (na \ me N or name CA or name C or name O or name CB )) or resid 71 through 132 or res \ id 134 through 143 or resid 153 through 183 or (resid 184 through 186 and (name \ N or name CA or name C or name O or name CB )) or resid 187 through 198 or resid \ 204 through 217 or (resid 218 through 220 and (name N or name CA or name C or n \ ame O or name CB )) or resid 221 through 242 or (resid 243 and (name N or name C \ A or name C or name O or name CB )) or resid 244 through 351 or resid 353 throug \ h 391 or resid 394 through 399 or (resid 401 and (name N or name CA or name C or \ name O or name CB )) or resid 402 through 407 or (resid 408 through 409 and (na \ me N or name CA or name C or name O or name CB )) or resid 410 through 411 or re \ sid 417 through 418 or (resid 419 and (name N or name CA or name C or name O or \ name CB )) or resid 420 through 495 or (resid 496 through 499 and (name N or nam \ e CA or name C or name O or name CB )) or resid 500 through 507 or (resid 508 an \ d (name N or name CA or name C or name O or name CB )) or resid 509 through 534 \ or (resid 535 through 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 578 or (resid 579 through 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 through 588)) selection = (chain 'B' and (resid 60 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 143 or (resid 153 through 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 163 \ or (resid 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 173 or (resid 174 and (name N or name CA or name C or name O or nam \ e CB )) or resid 175 through 185 or (resid 186 and (name N or name CA or name C \ or name O or name CB )) or resid 187 through 274 or (resid 275 and (name N or na \ me CA or name C or name O or name CB )) or resid 276 through 330 or (resid 331 a \ nd (name N or name CA or name C or name O or name CB )) or resid 332 through 382 \ or (resid 383 and (name N or name CA or name C or name O or name CB )) or resid \ 384 through 386 or (resid 387 and (name N or name CA or name C or name O or nam \ e CB )) or resid 388 through 399 or resid 401 through 455 or (resid 456 and (nam \ e N or name CA or name C or name O or name CB )) or resid 457 through 500 or res \ id 503 through 504 or (resid 505 and (name N or name CA or name C or name O or n \ ame CB )) or resid 506 through 518 or (resid 519 and (name N or name CA or name \ C or name O or name CB )) or resid 520 through 536 or (resid 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 552 or (resid 553 \ through 556 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 57 through 573 or (resid 574 and (name N or name CA or name C or name O or name \ CB )) or resid 575 through 582 or (resid 583 and (name N or name CA or name C or \ name O or name CB )) or resid 584 through 588)) } ncs_group { reference = (chain 'C' and (resid 5 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB )) or resid 31 through 32 or (resid 33 and (nam \ e N or name CA or name C or name O or name CB )) or resid 34 through 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 40 or (resid 41 and (name N or name CA or name C or name O or name CB )) or re \ sid 42 through 78 or resid 80 through 101 or (resid 102 through 118 and (name N \ or name CA or name C or name O or name CB )) or resid 119 through 162)) selection = (chain 'D' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 102 or resid 116 through 162)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.000 Extract box with map and model: 8.660 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.900 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9963 Z= 0.276 Angle : 0.814 11.905 13567 Z= 0.461 Chirality : 0.046 0.253 1610 Planarity : 0.007 0.144 1717 Dihedral : 13.926 85.934 3431 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1270 helix: 0.24 (0.24), residues: 446 sheet: -0.61 (0.42), residues: 153 loop : -1.31 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 364 HIS 0.005 0.001 HIS A 267 PHE 0.023 0.002 PHE D 125 TYR 0.014 0.002 TYR A 432 ARG 0.008 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.135 Fit side-chains REVERT: B 379 ARG cc_start: 0.7960 (tpt90) cc_final: 0.7752 (tpt-90) REVERT: D 90 MET cc_start: 0.8642 (tpt) cc_final: 0.8415 (tpt) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2851 time to fit residues: 58.7975 Evaluate side-chains 124 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN D 134 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9963 Z= 0.228 Angle : 0.658 9.137 13567 Z= 0.331 Chirality : 0.045 0.184 1610 Planarity : 0.005 0.095 1717 Dihedral : 5.253 34.120 1366 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 1.10 % Allowed : 9.26 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.72 (0.23), residues: 1270 helix: 0.65 (0.24), residues: 458 sheet: -0.41 (0.40), residues: 168 loop : -1.35 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 228 HIS 0.005 0.001 HIS A 267 PHE 0.024 0.002 PHE B 79 TYR 0.014 0.001 TYR C 40 ARG 0.007 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.103 Fit side-chains REVERT: B 379 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7864 (tpt90) REVERT: B 469 LYS cc_start: 0.5588 (ttmt) cc_final: 0.4377 (pttm) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 0.2334 time to fit residues: 43.9834 Evaluate side-chains 119 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 405 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9963 Z= 0.230 Angle : 0.633 8.311 13567 Z= 0.321 Chirality : 0.044 0.189 1610 Planarity : 0.005 0.074 1717 Dihedral : 5.098 28.972 1366 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 1.89 % Allowed : 12.05 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.75 (0.23), residues: 1270 helix: 0.69 (0.24), residues: 458 sheet: -0.72 (0.39), residues: 167 loop : -1.31 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 228 HIS 0.004 0.001 HIS A 267 PHE 0.019 0.002 PHE B 588 TYR 0.011 0.001 TYR C 40 ARG 0.004 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: B 379 ARG cc_start: 0.8210 (tpt90) cc_final: 0.7712 (tpt90) REVERT: A 120 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8158 (p0) REVERT: A 525 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7449 (mtp85) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 0.2291 time to fit residues: 45.0735 Evaluate side-chains 136 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 287 GLN B 305 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9963 Z= 0.408 Angle : 0.709 8.093 13567 Z= 0.361 Chirality : 0.047 0.197 1610 Planarity : 0.005 0.073 1717 Dihedral : 5.403 31.993 1366 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 2.59 % Allowed : 14.94 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -1.13 (0.23), residues: 1270 helix: 0.25 (0.24), residues: 462 sheet: -0.71 (0.41), residues: 161 loop : -1.51 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 228 HIS 0.006 0.001 HIS B 530 PHE 0.022 0.003 PHE D 67 TYR 0.014 0.002 TYR B 432 ARG 0.005 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.950 Fit side-chains REVERT: B 364 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: D 15 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: A 120 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8100 (p0) REVERT: A 213 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 386 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 525 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7363 (mtp85) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.2377 time to fit residues: 48.4410 Evaluate side-chains 136 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9963 Z= 0.234 Angle : 0.628 8.648 13567 Z= 0.320 Chirality : 0.044 0.229 1610 Planarity : 0.005 0.062 1717 Dihedral : 5.140 28.005 1366 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 3.88 % Allowed : 16.14 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1270 helix: 0.57 (0.24), residues: 461 sheet: -0.95 (0.40), residues: 157 loop : -1.45 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 228 HIS 0.004 0.001 HIS A 267 PHE 0.014 0.002 PHE B 588 TYR 0.009 0.001 TYR B 456 ARG 0.005 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7718 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: B 486 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 79 PHE cc_start: 0.7639 (m-10) cc_final: 0.7342 (m-10) REVERT: A 120 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8178 (p0) REVERT: A 213 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 386 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 525 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7359 (mtp85) outliers start: 39 outliers final: 19 residues processed: 161 average time/residue: 0.2296 time to fit residues: 51.2797 Evaluate side-chains 146 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9963 Z= 0.236 Angle : 0.627 8.419 13567 Z= 0.319 Chirality : 0.044 0.187 1610 Planarity : 0.005 0.056 1717 Dihedral : 5.038 24.185 1366 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 3.98 % Allowed : 16.33 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1270 helix: 0.64 (0.24), residues: 460 sheet: -0.83 (0.42), residues: 141 loop : -1.46 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 228 HIS 0.004 0.001 HIS B 306 PHE 0.014 0.002 PHE D 67 TYR 0.010 0.001 TYR A 335 ARG 0.010 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: B 366 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7641 (mtpt) REVERT: B 486 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8565 (mt) REVERT: D 15 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: A 120 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8132 (p0) REVERT: A 386 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 525 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7347 (mtp85) outliers start: 40 outliers final: 27 residues processed: 155 average time/residue: 0.2421 time to fit residues: 51.6426 Evaluate side-chains 154 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 75 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9963 Z= 0.175 Angle : 0.593 7.792 13567 Z= 0.301 Chirality : 0.043 0.199 1610 Planarity : 0.004 0.054 1717 Dihedral : 4.758 22.883 1366 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 3.69 % Allowed : 17.93 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.63 (0.23), residues: 1270 helix: 0.89 (0.24), residues: 465 sheet: -0.74 (0.42), residues: 147 loop : -1.32 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 228 HIS 0.006 0.001 HIS A 267 PHE 0.014 0.001 PHE B 588 TYR 0.011 0.001 TYR A 335 ARG 0.008 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 275 GLN cc_start: 0.7245 (tp40) cc_final: 0.7031 (tp-100) REVERT: B 364 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: B 366 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7686 (mtpt) REVERT: B 486 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8518 (mt) REVERT: B 541 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7326 (pp) REVERT: D 15 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: A 79 PHE cc_start: 0.7837 (m-10) cc_final: 0.7451 (m-10) REVERT: A 364 TRP cc_start: 0.6317 (OUTLIER) cc_final: 0.5932 (m-10) REVERT: A 386 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 525 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7470 (mtp85) outliers start: 37 outliers final: 22 residues processed: 154 average time/residue: 0.2211 time to fit residues: 48.7023 Evaluate side-chains 146 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9963 Z= 0.283 Angle : 0.649 10.262 13567 Z= 0.324 Chirality : 0.045 0.190 1610 Planarity : 0.005 0.055 1717 Dihedral : 4.875 21.478 1364 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 3.78 % Allowed : 17.63 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.85 (0.23), residues: 1270 helix: 0.67 (0.24), residues: 463 sheet: -0.75 (0.42), residues: 151 loop : -1.45 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 228 HIS 0.006 0.001 HIS A 267 PHE 0.018 0.002 PHE D 67 TYR 0.011 0.001 TYR A 211 ARG 0.004 0.001 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: B 170 GLU cc_start: 0.5030 (tt0) cc_final: 0.4674 (tt0) REVERT: B 364 TRP cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: B 366 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7706 (mtpt) REVERT: B 467 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7264 (t-90) REVERT: B 486 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 541 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7336 (pp) REVERT: D 15 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.5993 (mp0) REVERT: A 79 PHE cc_start: 0.7890 (m-10) cc_final: 0.7609 (m-10) REVERT: A 337 LEU cc_start: 0.8358 (tt) cc_final: 0.7471 (mp) REVERT: A 344 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6834 (mtm-85) REVERT: A 525 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6834 (mtp85) outliers start: 38 outliers final: 27 residues processed: 152 average time/residue: 0.2344 time to fit residues: 49.0350 Evaluate side-chains 149 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 570 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.0670 chunk 107 optimal weight: 0.0170 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9963 Z= 0.188 Angle : 0.614 9.809 13567 Z= 0.305 Chirality : 0.043 0.190 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.701 21.836 1364 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 3.59 % Allowed : 17.93 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.73 (0.23), residues: 1270 helix: 0.85 (0.24), residues: 462 sheet: -0.87 (0.41), residues: 147 loop : -1.38 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 228 HIS 0.007 0.001 HIS A 267 PHE 0.013 0.002 PHE B 588 TYR 0.011 0.001 TYR A 335 ARG 0.004 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: B 275 GLN cc_start: 0.7281 (tp40) cc_final: 0.7039 (tp-100) REVERT: B 364 TRP cc_start: 0.7780 (OUTLIER) cc_final: 0.7572 (m-10) REVERT: B 366 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7711 (mtpt) REVERT: B 467 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: B 486 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 541 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7317 (pp) REVERT: D 15 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.5955 (mp0) REVERT: A 263 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8241 (mt) REVERT: A 337 LEU cc_start: 0.8307 (tt) cc_final: 0.7455 (mp) REVERT: A 525 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6865 (mtp85) outliers start: 36 outliers final: 22 residues processed: 154 average time/residue: 0.2280 time to fit residues: 50.3669 Evaluate side-chains 149 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 0.0070 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9963 Z= 0.236 Angle : 0.648 12.883 13567 Z= 0.321 Chirality : 0.044 0.202 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.728 21.374 1364 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 3.19 % Allowed : 17.83 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.77 (0.23), residues: 1270 helix: 0.79 (0.24), residues: 460 sheet: -0.92 (0.41), residues: 147 loop : -1.37 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 228 HIS 0.007 0.001 HIS A 267 PHE 0.014 0.002 PHE B 588 TYR 0.009 0.001 TYR A 109 ARG 0.004 0.001 ARG D 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: B 364 TRP cc_start: 0.7823 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: B 366 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7714 (mtpt) REVERT: B 467 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7241 (t-90) REVERT: B 486 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8582 (mt) REVERT: B 541 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7325 (pp) REVERT: D 15 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: A 337 LEU cc_start: 0.8302 (tt) cc_final: 0.7443 (mp) REVERT: A 364 TRP cc_start: 0.6409 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: A 386 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 525 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6874 (mtp85) outliers start: 32 outliers final: 23 residues processed: 144 average time/residue: 0.2094 time to fit residues: 42.9528 Evaluate side-chains 151 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 364 TRP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 364 TRP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.0020 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177590 restraints weight = 10728.493| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.47 r_work: 0.3828 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9963 Z= 0.227 Angle : 0.640 12.200 13567 Z= 0.317 Chirality : 0.044 0.193 1610 Planarity : 0.005 0.054 1717 Dihedral : 4.697 21.185 1364 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 3.29 % Allowed : 17.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.49 % 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: -0.73 (0.23), residues: 1270 helix: 0.84 (0.24), residues: 462 sheet: -0.97 (0.41), residues: 147 loop : -1.35 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 228 HIS 0.007 0.001 HIS A 267 PHE 0.013 0.002 PHE B 588 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.001 ARG D 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.42 seconds wall clock time: 41 minutes 10.25 seconds (2470.25 seconds total)