Starting phenix.real_space_refine on Fri Jul 19 07:37:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jje_36345/07_2024/8jje_36345_neut.cif" } resolution = 3.4 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= 0.030 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 40 5.16 5 C 4245 2.51 5 N 1079 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4881 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' ZN': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.68 Number of scatterers: 6670 At special positions: 0 Unit cell: (93.84, 82.11, 119.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 40 16.00 O 1305 8.00 N 1079 7.00 C 4245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.06 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.11 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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 Links applied ALPHA1-3 " MAN E 4 " - " MAN E 5 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1001 " - " ASN A 432 " Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 374 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 59.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 4.418A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.744A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.277A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.052A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.554A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.737A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.865A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.668A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.804A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.621A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.691A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 405 removed outlier: 4.491A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.534A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.682A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.595A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.802A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.407A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.627A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.848A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.966A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.621A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.988A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.881A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.142A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.720A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.248A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.281A pdb=" N MET A 332 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A 362 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR A 334 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.012A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 298 hydrogen bonds defined for protein. 834 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: 1.81 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1349 1.33 - 1.46: 2208 1.46 - 1.59: 3231 1.59 - 1.72: 0 1.72 - 1.84: 60 Bond restraints: 6848 Sorted by residual: bond pdb=" CD GLU A 375 " pdb=" OE2 GLU A 375 " ideal model delta sigma weight residual 1.249 1.469 -0.220 1.90e-02 2.77e+03 1.34e+02 bond pdb=" O3 SO4 A1003 " pdb=" S SO4 A1003 " ideal model delta sigma weight residual 1.499 1.396 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O1 SO4 A1003 " pdb=" S SO4 A1003 " ideal model delta sigma weight residual 1.498 1.403 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.310 0.044 1.10e-02 8.26e+03 1.57e+01 bond pdb=" CG HIS A 378 " pdb=" CD2 HIS A 378 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.34e+01 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.83: 201 105.83 - 113.21: 3289 113.21 - 120.59: 3257 120.59 - 127.97: 2492 127.97 - 135.35: 70 Bond angle restraints: 9309 Sorted by residual: angle pdb=" CA VAL A 172 " pdb=" CB VAL A 172 " pdb=" CG1 VAL A 172 " ideal model delta sigma weight residual 110.40 121.14 -10.74 1.70e+00 3.46e-01 3.99e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 112.60 117.70 -5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" CA ASN B 501 " pdb=" CB ASN B 501 " pdb=" CG ASN B 501 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " pdb=" CG ASN A 394 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 ... (remaining 9304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 3956 21.28 - 42.56: 231 42.56 - 63.84: 42 63.84 - 85.13: 27 85.13 - 106.41: 13 Dihedral angle restraints: 4269 sinusoidal: 1940 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -175.43 89.43 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -140.68 54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA ILE A 544 " pdb=" C ILE A 544 " pdb=" N SER A 545 " pdb=" CA SER A 545 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 990 0.189 - 0.377: 31 0.377 - 0.566: 2 0.566 - 0.755: 0 0.755 - 0.944: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.37e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.36e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 1021 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " 0.083 2.00e-02 2.50e+03 3.94e-02 3.88e+01 pdb=" CG TRP A 477 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 207 " -0.080 2.00e-02 2.50e+03 4.16e-02 3.45e+01 pdb=" CG TYR A 207 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 207 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 207 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 207 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 207 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 207 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 207 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " -0.054 2.00e-02 2.50e+03 4.65e-02 3.24e+01 pdb=" CG HIS A 374 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.064 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 5 2.44 - 3.06: 4056 3.06 - 3.67: 9575 3.67 - 4.29: 15004 4.29 - 4.90: 24595 Nonbonded interactions: 53235 Sorted by model distance: nonbonded pdb="ZN ZN A1002 " pdb=" O HOH A1101 " model vdw 1.829 2.230 nonbonded pdb="ZN ZN A1002 " pdb=" O1 SO4 A1003 " model vdw 1.965 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A1002 " model vdw 2.178 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A1002 " model vdw 2.180 2.230 nonbonded pdb=" OE2 GLU A 375 " pdb=" O HOH A1101 " model vdw 2.356 2.440 ... (remaining 53230 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 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.780 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.011 0.220 6848 Z= 0.707 Angle : 1.507 14.008 9309 Z= 0.979 Chirality : 0.093 0.944 1024 Planarity : 0.014 0.225 1180 Dihedral : 16.243 106.406 2754 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 5.44 % Favored : 92.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.26), residues: 790 helix: -1.73 (0.20), residues: 393 sheet: 1.63 (0.86), residues: 35 loop : -0.99 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.012 TRP A 477 HIS 0.035 0.006 HIS A 374 PHE 0.065 0.010 PHE A 400 TYR 0.080 0.013 TYR A 207 ARG 0.023 0.003 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8611 (tp40) cc_final: 0.8243 (mm110) REVERT: A 54 ILE cc_start: 0.7943 (mt) cc_final: 0.7718 (mt) REVERT: A 131 LYS cc_start: 0.6917 (ptpt) cc_final: 0.6580 (mtpt) REVERT: A 152 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: A 171 GLU cc_start: 0.7739 (tp30) cc_final: 0.7131 (tm-30) REVERT: A 207 TYR cc_start: 0.8687 (m-80) cc_final: 0.8153 (m-80) REVERT: A 331 SER cc_start: 0.9128 (m) cc_final: 0.8907 (p) REVERT: A 343 CYS cc_start: 0.8237 (m) cc_final: 0.7752 (t) REVERT: A 360 MET cc_start: 0.9072 (ttt) cc_final: 0.8854 (ttt) REVERT: A 428 PHE cc_start: 0.7962 (t80) cc_final: 0.7730 (t80) REVERT: A 475 LYS cc_start: 0.8365 (tttt) cc_final: 0.8147 (tmmt) REVERT: B 346 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8163 (ptm-80) REVERT: B 382 VAL cc_start: 0.7925 (t) cc_final: 0.7545 (t) REVERT: B 408 ARG cc_start: 0.9037 (ptm160) cc_final: 0.8330 (ppt170) REVERT: B 428 ASP cc_start: 0.8683 (t0) cc_final: 0.8406 (p0) REVERT: B 484 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8405 (mt-10) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2048 time to fit residues: 37.4070 Evaluate side-chains 86 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6848 Z= 0.193 Angle : 0.659 6.725 9309 Z= 0.336 Chirality : 0.045 0.401 1024 Planarity : 0.004 0.038 1180 Dihedral : 12.293 80.929 1245 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.01 % Allowed : 9.46 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.37 (0.29), residues: 790 helix: -0.01 (0.26), residues: 398 sheet: 0.91 (0.77), residues: 46 loop : -0.55 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.005 0.001 HIS A 378 PHE 0.029 0.002 PHE B 486 TYR 0.016 0.002 TYR A 385 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8257 (mmm) REVERT: A 207 TYR cc_start: 0.8623 (m-80) cc_final: 0.7964 (m-80) REVERT: A 360 MET cc_start: 0.9036 (ttt) cc_final: 0.8794 (ttt) REVERT: B 346 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8066 (ppt170) REVERT: B 382 VAL cc_start: 0.7510 (t) cc_final: 0.7161 (t) REVERT: B 398 ASP cc_start: 0.9018 (m-30) cc_final: 0.8811 (m-30) REVERT: B 408 ARG cc_start: 0.8954 (ptm160) cc_final: 0.8135 (ppt170) REVERT: B 484 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8446 (mt-10) REVERT: B 486 PHE cc_start: 0.8011 (t80) cc_final: 0.7699 (t80) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.1733 time to fit residues: 24.0198 Evaluate side-chains 80 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 277 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6848 Z= 0.153 Angle : 0.570 7.046 9309 Z= 0.281 Chirality : 0.043 0.318 1024 Planarity : 0.004 0.057 1180 Dihedral : 9.738 63.946 1245 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.58 % Allowed : 11.17 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.04 (0.29), residues: 790 helix: 0.50 (0.27), residues: 400 sheet: 0.80 (0.80), residues: 44 loop : -0.54 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS A 378 PHE 0.033 0.002 PHE B 486 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 188 ASN cc_start: 0.8359 (m-40) cc_final: 0.7774 (t0) REVERT: A 198 ASP cc_start: 0.8341 (p0) cc_final: 0.8132 (p0) REVERT: A 207 TYR cc_start: 0.8550 (m-80) cc_final: 0.7953 (m-80) REVERT: A 440 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 346 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8058 (ppt170) REVERT: B 408 ARG cc_start: 0.8938 (ptm160) cc_final: 0.8254 (ppt170) outliers start: 25 outliers final: 14 residues processed: 97 average time/residue: 0.1770 time to fit residues: 23.5781 Evaluate side-chains 81 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6848 Z= 0.187 Angle : 0.566 10.570 9309 Z= 0.275 Chirality : 0.043 0.298 1024 Planarity : 0.004 0.039 1180 Dihedral : 8.229 57.377 1242 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.72 % Allowed : 12.46 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.10 (0.30), residues: 790 helix: 0.60 (0.27), residues: 402 sheet: 0.51 (0.80), residues: 44 loop : -0.53 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS A 378 PHE 0.022 0.002 PHE A 369 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 188 ASN cc_start: 0.8337 (m-40) cc_final: 0.7764 (t0) REVERT: A 207 TYR cc_start: 0.8471 (m-80) cc_final: 0.7892 (m-80) REVERT: A 440 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 346 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7957 (ppt170) REVERT: B 408 ARG cc_start: 0.8931 (ptm160) cc_final: 0.8262 (ppt170) REVERT: B 417 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8419 (mttt) outliers start: 26 outliers final: 19 residues processed: 94 average time/residue: 0.1892 time to fit residues: 23.8436 Evaluate side-chains 89 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 31 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6848 Z= 0.170 Angle : 0.517 5.182 9309 Z= 0.255 Chirality : 0.042 0.287 1024 Planarity : 0.004 0.044 1180 Dihedral : 7.446 59.601 1242 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.44 % Allowed : 13.18 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.26 (0.30), residues: 790 helix: 0.78 (0.27), residues: 402 sheet: 0.43 (0.81), residues: 44 loop : -0.51 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.020 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8417 (m-80) cc_final: 0.7816 (m-80) REVERT: A 440 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8270 (tm) REVERT: A 469 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7354 (Cg_endo) REVERT: B 346 ARG cc_start: 0.8440 (ttm110) cc_final: 0.8040 (ppt170) REVERT: B 408 ARG cc_start: 0.8940 (ptm160) cc_final: 0.8292 (ppt170) REVERT: B 417 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8258 (mttt) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 0.1838 time to fit residues: 22.7174 Evaluate side-chains 90 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.7967 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6848 Z= 0.162 Angle : 0.519 7.470 9309 Z= 0.253 Chirality : 0.041 0.270 1024 Planarity : 0.004 0.045 1180 Dihedral : 7.029 56.080 1242 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 14.33 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.30), residues: 790 helix: 0.86 (0.27), residues: 405 sheet: 0.40 (0.80), residues: 44 loop : -0.52 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.002 0.001 HIS A 374 PHE 0.019 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8384 (m-80) cc_final: 0.7772 (m-80) REVERT: A 440 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 469 PRO cc_start: 0.7659 (Cg_exo) cc_final: 0.7428 (Cg_endo) REVERT: B 346 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8023 (ppt170) REVERT: B 387 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8492 (mt) REVERT: B 408 ARG cc_start: 0.8927 (ptm160) cc_final: 0.8291 (ppt170) REVERT: B 417 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8332 (mttt) outliers start: 24 outliers final: 16 residues processed: 96 average time/residue: 0.1843 time to fit residues: 24.0077 Evaluate side-chains 95 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6848 Z= 0.208 Angle : 0.528 5.134 9309 Z= 0.261 Chirality : 0.042 0.271 1024 Planarity : 0.004 0.047 1180 Dihedral : 6.632 48.300 1239 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 14.18 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.25 (0.30), residues: 790 helix: 0.84 (0.27), residues: 406 sheet: 0.19 (0.79), residues: 46 loop : -0.58 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.002 PHE A 369 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8381 (m-80) cc_final: 0.7782 (m-80) REVERT: A 440 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7986 (tp) REVERT: B 346 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8016 (ppt170) REVERT: B 387 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8511 (mt) REVERT: B 408 ARG cc_start: 0.8923 (ptm160) cc_final: 0.8291 (ppt170) REVERT: B 417 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8326 (mttt) outliers start: 24 outliers final: 19 residues processed: 97 average time/residue: 0.1887 time to fit residues: 24.5623 Evaluate side-chains 93 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.0000 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6848 Z= 0.162 Angle : 0.507 5.338 9309 Z= 0.249 Chirality : 0.041 0.264 1024 Planarity : 0.004 0.048 1180 Dihedral : 6.450 47.752 1239 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.01 % Allowed : 14.90 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.30), residues: 790 helix: 0.92 (0.27), residues: 407 sheet: 0.06 (0.78), residues: 46 loop : -0.54 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.018 0.001 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8369 (m-80) cc_final: 0.7781 (m-80) REVERT: A 440 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7920 (tp) REVERT: B 346 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8025 (ppt170) REVERT: B 387 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 408 ARG cc_start: 0.8892 (ptm160) cc_final: 0.8260 (ppt170) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.1877 time to fit residues: 23.5952 Evaluate side-chains 90 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6848 Z= 0.173 Angle : 0.513 6.590 9309 Z= 0.253 Chirality : 0.041 0.264 1024 Planarity : 0.004 0.048 1180 Dihedral : 6.315 47.810 1238 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.15 % Allowed : 15.19 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.37 (0.30), residues: 790 helix: 0.97 (0.27), residues: 407 sheet: 0.06 (0.78), residues: 46 loop : -0.55 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.020 0.001 PHE A 369 TYR 0.011 0.001 TYR A 385 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8367 (m-80) cc_final: 0.7769 (m-80) REVERT: A 228 HIS cc_start: 0.7671 (t70) cc_final: 0.7267 (m-70) REVERT: A 440 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7939 (tp) REVERT: B 346 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7971 (ppt170) REVERT: B 387 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8530 (mt) REVERT: B 408 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8220 (ppt170) REVERT: B 417 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8250 (mttt) outliers start: 22 outliers final: 18 residues processed: 95 average time/residue: 0.2265 time to fit residues: 29.2447 Evaluate side-chains 95 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6848 Z= 0.199 Angle : 0.546 12.871 9309 Z= 0.269 Chirality : 0.042 0.268 1024 Planarity : 0.004 0.047 1180 Dihedral : 6.291 47.787 1238 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.15 % Allowed : 15.19 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.43 (0.30), residues: 790 helix: 1.01 (0.27), residues: 407 sheet: 0.07 (0.79), residues: 46 loop : -0.50 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.019 0.001 PHE A 369 TYR 0.011 0.001 TYR A 385 ARG 0.007 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8366 (m-80) cc_final: 0.7761 (m-80) REVERT: A 228 HIS cc_start: 0.7688 (t70) cc_final: 0.7271 (m-70) REVERT: A 440 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 455 MET cc_start: 0.7848 (tmm) cc_final: 0.6932 (tmm) REVERT: B 346 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7933 (ppt170) REVERT: B 366 SER cc_start: 0.8675 (t) cc_final: 0.8417 (p) REVERT: B 387 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (mt) REVERT: B 408 ARG cc_start: 0.8833 (ptm160) cc_final: 0.8207 (ppt170) REVERT: B 417 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8224 (mttt) outliers start: 22 outliers final: 19 residues processed: 95 average time/residue: 0.2016 time to fit residues: 25.5081 Evaluate side-chains 96 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120976 restraints weight = 9850.413| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.65 r_work: 0.3381 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6848 Z= 0.202 Angle : 0.538 8.746 9309 Z= 0.266 Chirality : 0.042 0.259 1024 Planarity : 0.004 0.047 1180 Dihedral : 6.272 48.106 1238 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.30 % Allowed : 14.90 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.43 (0.30), residues: 790 helix: 1.02 (0.27), residues: 407 sheet: 0.06 (0.79), residues: 46 loop : -0.52 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.022 0.001 PHE A 369 TYR 0.011 0.001 TYR A 385 ARG 0.008 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.82 seconds wall clock time: 31 minutes 51.17 seconds (1911.17 seconds total)