Starting phenix.real_space_refine on Thu Mar 14 19:30:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqy_26702/03_2024/7uqy_26702_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.035 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 P 2 5.49 5 S 46 5.16 5 C 6148 2.51 5 N 1612 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 129": "OE1" <-> "OE2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4750 Classifications: {'peptide': 582} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 554} Chain breaks: 3 Chain: "B" Number of atoms: 4742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4742 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.63, per 1000 atoms: 0.59 Number of scatterers: 9556 At special positions: 0 Unit cell: (102.672, 87.768, 111.78, 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) S 46 16.00 P 2 15.00 O 1748 8.00 N 1612 7.00 C 6148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.04 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 637 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 13 sheets defined 32.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.806A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.677A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 327 No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.784A pdb=" N ARG A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.574A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.590A pdb=" N HIS A 636 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.671A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.510A pdb=" N GLU B 239 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.851A pdb=" N ASP B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.927A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 314' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.518A pdb=" N ALA B 337 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.721A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.894A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 519 through 523 removed outlier: 4.050A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.768A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 614 through 623 removed outlier: 3.734A pdb=" N ASN B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP B 619 " --> pdb=" O ASP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 671 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.716A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.945A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA A 217 " --> pdb=" O ASN A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 269 removed outlier: 3.602A pdb=" N THR A 297 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.075A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 623 through 627 removed outlier: 3.506A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 485 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 596 through 600 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.925A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.736A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 254 through 257 Processing sheet with id= J, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 5.874A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 563 through 565 removed outlier: 3.703A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.623A pdb=" N GLU B 583 " --> pdb=" O LEU B 570 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 636 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: 2.63 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1529 1.32 - 1.45: 2807 1.45 - 1.57: 5405 1.57 - 1.70: 3 1.70 - 1.82: 71 Bond restraints: 9815 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.89e+01 bond pdb=" N ILE B 449 " pdb=" CA ILE B 449 " ideal model delta sigma weight residual 1.458 1.487 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" C PRO B 443 " pdb=" O PRO B 443 " ideal model delta sigma weight residual 1.237 1.194 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" N ASN B 442 " pdb=" CA ASN B 442 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.39e-02 5.18e+03 1.01e+01 bond pdb=" N PHE B 445 " pdb=" CA PHE B 445 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 7.00e+00 ... (remaining 9810 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.68: 248 105.68 - 112.80: 5165 112.80 - 119.92: 3356 119.92 - 127.05: 4433 127.05 - 134.17: 137 Bond angle restraints: 13339 Sorted by residual: angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.14 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.22 -4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O2A UDP A 801 " ideal model delta sigma weight residual 110.83 106.97 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 109.95 106.32 3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA TRP B 396 " pdb=" C TRP B 396 " pdb=" O TRP B 396 " ideal model delta sigma weight residual 120.55 116.95 3.60 1.07e+00 8.73e-01 1.13e+01 ... (remaining 13334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 5540 21.61 - 43.21: 329 43.21 - 64.82: 33 64.82 - 86.42: 17 86.42 - 108.03: 5 Dihedral angle restraints: 5924 sinusoidal: 2476 harmonic: 3448 Sorted by residual: dihedral pdb=" CB CYS B 85 " pdb=" SG CYS B 85 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual -86.00 -173.57 87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 151 " pdb=" CB CYS B 151 " ideal model delta sinusoidal sigma weight residual 93.00 9.45 83.55 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual 93.00 150.67 -57.67 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1151 0.053 - 0.105: 252 0.105 - 0.158: 45 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 1451 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU B 160 " pdb=" CB LEU B 160 " pdb=" CD1 LEU B 160 " pdb=" CD2 LEU B 160 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 449 " pdb=" N ILE B 449 " pdb=" C ILE B 449 " pdb=" CB ILE B 449 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1448 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 697 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO B 698 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 698 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 698 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 395 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C PHE B 395 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE B 395 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 396 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 638 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO A 639 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.034 5.00e-02 4.00e+02 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 662 2.74 - 3.28: 9712 3.28 - 3.82: 16268 3.82 - 4.36: 19534 4.36 - 4.90: 33153 Nonbonded interactions: 79329 Sorted by model distance: nonbonded pdb=" OD2 ASP A 147 " pdb=" OG SER A 149 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 439 " pdb=" NZ LYS B 359 " model vdw 2.257 2.520 nonbonded pdb=" O GLU A 587 " pdb=" OH TYR A 630 " model vdw 2.263 2.440 nonbonded pdb=" N ASN A 254 " pdb=" OE2 GLU B 532 " model vdw 2.279 2.520 ... (remaining 79324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 3.980 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 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 : 0.003 0.068 9815 Z= 0.203 Angle : 0.591 7.160 13339 Z= 0.321 Chirality : 0.045 0.263 1451 Planarity : 0.005 0.075 1694 Dihedral : 13.643 108.028 3669 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.18 (0.25), residues: 1151 helix: 0.74 (0.28), residues: 359 sheet: -0.35 (0.42), residues: 152 loop : -0.50 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 619 HIS 0.005 0.001 HIS B 88 PHE 0.010 0.001 PHE A 250 TYR 0.018 0.001 TYR B 582 ARG 0.010 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.180 Fit side-chains REVERT: A 250 PHE cc_start: 0.6037 (t80) cc_final: 0.5787 (t80) REVERT: A 265 VAL cc_start: 0.6249 (m) cc_final: 0.4518 (t) REVERT: B 92 ASP cc_start: 0.7698 (t0) cc_final: 0.7492 (t70) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 1.0088 time to fit residues: 264.3425 Evaluate side-chains 213 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 185 ASN A 189 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9815 Z= 0.254 Angle : 0.584 7.865 13339 Z= 0.291 Chirality : 0.045 0.149 1451 Planarity : 0.004 0.059 1694 Dihedral : 8.138 103.285 1377 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.73 % Allowed : 11.60 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.18 (0.25), residues: 1151 helix: 0.59 (0.28), residues: 364 sheet: -0.34 (0.42), residues: 153 loop : -0.41 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 374 HIS 0.004 0.001 HIS B 601 PHE 0.019 0.002 PHE B 652 TYR 0.023 0.002 TYR B 582 ARG 0.007 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6375 (m) cc_final: 0.4571 (t) REVERT: B 174 MET cc_start: 0.4885 (OUTLIER) cc_final: 0.4286 (mtt) REVERT: B 573 TRP cc_start: 0.7809 (t-100) cc_final: 0.7537 (t-100) outliers start: 18 outliers final: 2 residues processed: 236 average time/residue: 1.0310 time to fit residues: 263.2694 Evaluate side-chains 222 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 412 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9815 Z= 0.201 Angle : 0.553 7.877 13339 Z= 0.273 Chirality : 0.044 0.139 1451 Planarity : 0.004 0.054 1694 Dihedral : 6.745 63.998 1375 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.40 % Allowed : 13.61 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1151 helix: 0.58 (0.28), residues: 371 sheet: -0.45 (0.44), residues: 140 loop : -0.34 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.003 0.001 HIS A 285 PHE 0.019 0.001 PHE B 400 TYR 0.020 0.001 TYR B 582 ARG 0.010 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6320 (m) cc_final: 0.4578 (t) REVERT: A 295 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7038 (mt) REVERT: A 413 GLU cc_start: 0.6564 (tt0) cc_final: 0.6306 (tt0) REVERT: A 653 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5840 (pt0) REVERT: B 174 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4148 (mtt) REVERT: B 307 ASP cc_start: 0.6107 (OUTLIER) cc_final: 0.5782 (p0) REVERT: B 310 GLN cc_start: 0.7348 (mp10) cc_final: 0.6958 (mp10) REVERT: B 427 GLU cc_start: 0.6239 (mp0) cc_final: 0.6038 (mp0) REVERT: B 573 TRP cc_start: 0.7818 (t-100) cc_final: 0.7612 (t-100) outliers start: 25 outliers final: 6 residues processed: 232 average time/residue: 1.0182 time to fit residues: 256.0125 Evaluate side-chains 222 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9815 Z= 0.195 Angle : 0.548 7.794 13339 Z= 0.270 Chirality : 0.043 0.139 1451 Planarity : 0.004 0.051 1694 Dihedral : 6.218 61.319 1375 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.88 % Allowed : 15.72 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.25), residues: 1151 helix: 0.79 (0.28), residues: 359 sheet: -0.47 (0.44), residues: 141 loop : -0.41 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 374 HIS 0.003 0.000 HIS A 285 PHE 0.024 0.001 PHE B 400 TYR 0.021 0.001 TYR B 582 ARG 0.008 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6310 (m) cc_final: 0.4518 (t) REVERT: A 413 GLU cc_start: 0.6512 (tt0) cc_final: 0.6229 (tt0) REVERT: A 653 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5864 (pt0) REVERT: B 174 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4178 (mtt) outliers start: 30 outliers final: 8 residues processed: 231 average time/residue: 0.9849 time to fit residues: 246.9810 Evaluate side-chains 220 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 28 optimal weight: 0.0270 overall best weight: 0.2272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9815 Z= 0.155 Angle : 0.567 11.988 13339 Z= 0.273 Chirality : 0.042 0.142 1451 Planarity : 0.004 0.049 1694 Dihedral : 5.826 60.154 1375 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.40 % Allowed : 16.49 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.07 (0.25), residues: 1151 helix: 0.88 (0.29), residues: 359 sheet: -0.33 (0.43), residues: 144 loop : -0.46 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 396 HIS 0.019 0.001 HIS B 88 PHE 0.024 0.001 PHE B 400 TYR 0.022 0.001 TYR B 582 ARG 0.009 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 225 time to evaluate : 1.095 Fit side-chains REVERT: A 653 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5856 (pt0) REVERT: B 473 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7492 (tp) REVERT: B 516 GLU cc_start: 0.6066 (mp0) cc_final: 0.5660 (mp0) outliers start: 25 outliers final: 10 residues processed: 236 average time/residue: 0.9934 time to fit residues: 254.4872 Evaluate side-chains 232 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9815 Z= 0.247 Angle : 0.599 9.049 13339 Z= 0.293 Chirality : 0.044 0.179 1451 Planarity : 0.004 0.051 1694 Dihedral : 5.953 61.269 1375 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.40 % Allowed : 17.93 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.08 (0.25), residues: 1151 helix: 0.83 (0.28), residues: 360 sheet: -0.22 (0.45), residues: 138 loop : -0.47 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 619 HIS 0.020 0.001 HIS B 88 PHE 0.029 0.002 PHE B 400 TYR 0.021 0.002 TYR B 582 ARG 0.005 0.000 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.030 Fit side-chains REVERT: A 169 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: A 265 VAL cc_start: 0.6521 (m) cc_final: 0.4742 (t) REVERT: A 413 GLU cc_start: 0.6558 (tt0) cc_final: 0.6345 (tt0) REVERT: A 653 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5929 (pt0) REVERT: A 664 VAL cc_start: 0.8274 (m) cc_final: 0.8054 (t) REVERT: B 177 LEU cc_start: 0.5241 (tt) cc_final: 0.5025 (tt) REVERT: B 307 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5765 (p0) REVERT: B 516 GLU cc_start: 0.6119 (mp0) cc_final: 0.5702 (mp0) outliers start: 25 outliers final: 12 residues processed: 232 average time/residue: 0.9853 time to fit residues: 248.2409 Evaluate side-chains 228 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 213 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9815 Z= 0.280 Angle : 0.616 9.077 13339 Z= 0.304 Chirality : 0.045 0.164 1451 Planarity : 0.004 0.050 1694 Dihedral : 6.151 58.950 1375 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.59 % Allowed : 18.98 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.15 (0.25), residues: 1151 helix: 0.70 (0.28), residues: 372 sheet: -0.38 (0.44), residues: 145 loop : -0.45 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 374 HIS 0.017 0.001 HIS B 88 PHE 0.035 0.002 PHE B 400 TYR 0.019 0.002 TYR B 582 ARG 0.007 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.148 Fit side-chains REVERT: A 107 THR cc_start: 0.8867 (p) cc_final: 0.8657 (p) REVERT: A 169 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 250 PHE cc_start: 0.6175 (t80) cc_final: 0.5949 (t80) REVERT: A 265 VAL cc_start: 0.6565 (m) cc_final: 0.4846 (t) REVERT: A 295 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 413 GLU cc_start: 0.6548 (tt0) cc_final: 0.6317 (tt0) REVERT: A 653 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5942 (pt0) REVERT: A 664 VAL cc_start: 0.8272 (m) cc_final: 0.8061 (t) REVERT: B 177 LEU cc_start: 0.5295 (tt) cc_final: 0.5086 (tt) outliers start: 27 outliers final: 11 residues processed: 241 average time/residue: 0.9686 time to fit residues: 253.8041 Evaluate side-chains 228 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 214 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9815 Z= 0.273 Angle : 0.630 10.386 13339 Z= 0.312 Chirality : 0.045 0.152 1451 Planarity : 0.005 0.048 1694 Dihedral : 6.146 58.042 1375 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.49 % Allowed : 19.75 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.21 (0.25), residues: 1151 helix: 0.60 (0.28), residues: 372 sheet: -0.44 (0.44), residues: 145 loop : -0.45 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 619 HIS 0.015 0.001 HIS B 88 PHE 0.040 0.002 PHE B 551 TYR 0.020 0.002 TYR B 582 ARG 0.011 0.001 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 169 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 250 PHE cc_start: 0.6159 (t80) cc_final: 0.5924 (t80) REVERT: A 265 VAL cc_start: 0.6560 (m) cc_final: 0.4844 (t) REVERT: A 413 GLU cc_start: 0.6569 (tt0) cc_final: 0.6325 (tt0) REVERT: A 577 PHE cc_start: 0.5840 (t80) cc_final: 0.5390 (t80) REVERT: A 653 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5951 (pt0) REVERT: A 664 VAL cc_start: 0.8243 (m) cc_final: 0.8035 (t) REVERT: B 177 LEU cc_start: 0.5414 (tt) cc_final: 0.5166 (tt) REVERT: B 612 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6329 (ttp) outliers start: 26 outliers final: 13 residues processed: 236 average time/residue: 0.9759 time to fit residues: 250.5483 Evaluate side-chains 240 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS B 378 GLN ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9815 Z= 0.394 Angle : 0.695 12.756 13339 Z= 0.348 Chirality : 0.049 0.235 1451 Planarity : 0.005 0.049 1694 Dihedral : 6.569 59.083 1375 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.21 % Allowed : 20.71 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.25), residues: 1151 helix: 0.39 (0.27), residues: 366 sheet: -0.57 (0.42), residues: 155 loop : -0.55 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 374 HIS 0.014 0.001 HIS B 88 PHE 0.041 0.003 PHE B 400 TYR 0.018 0.002 TYR B 582 ARG 0.009 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: A 250 PHE cc_start: 0.6187 (t80) cc_final: 0.5917 (t80) REVERT: A 265 VAL cc_start: 0.6698 (m) cc_final: 0.5088 (t) REVERT: A 413 GLU cc_start: 0.6624 (tt0) cc_final: 0.6398 (tt0) REVERT: A 577 PHE cc_start: 0.5955 (t80) cc_final: 0.5504 (t80) REVERT: A 608 TYR cc_start: 0.6790 (t80) cc_final: 0.6491 (t80) REVERT: A 653 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: A 664 VAL cc_start: 0.8251 (m) cc_final: 0.8025 (t) REVERT: B 177 LEU cc_start: 0.5584 (tt) cc_final: 0.5374 (tt) REVERT: B 612 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6492 (ttp) outliers start: 23 outliers final: 13 residues processed: 242 average time/residue: 1.0130 time to fit residues: 265.5358 Evaluate side-chains 241 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9815 Z= 0.247 Angle : 0.651 9.913 13339 Z= 0.322 Chirality : 0.045 0.187 1451 Planarity : 0.005 0.049 1694 Dihedral : 6.256 59.886 1375 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.82 % Allowed : 21.86 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.36 (0.25), residues: 1151 helix: 0.54 (0.27), residues: 372 sheet: -0.55 (0.43), residues: 145 loop : -0.58 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 619 HIS 0.015 0.001 HIS B 88 PHE 0.047 0.002 PHE B 551 TYR 0.021 0.001 TYR B 582 ARG 0.012 0.001 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 265 VAL cc_start: 0.6612 (m) cc_final: 0.4930 (t) REVERT: A 413 GLU cc_start: 0.6583 (tt0) cc_final: 0.6229 (tt0) REVERT: A 577 PHE cc_start: 0.5873 (t80) cc_final: 0.5426 (t80) REVERT: A 608 TYR cc_start: 0.6700 (t80) cc_final: 0.6426 (t80) REVERT: A 653 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5980 (pt0) REVERT: A 664 VAL cc_start: 0.8215 (m) cc_final: 0.7988 (t) REVERT: B 129 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6800 (mm-30) REVERT: B 612 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6457 (ttp) outliers start: 19 outliers final: 11 residues processed: 230 average time/residue: 0.9833 time to fit residues: 245.3910 Evaluate side-chains 233 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 220 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 612 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS B 378 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.147562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130219 restraints weight = 13619.820| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.32 r_work: 0.3629 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9815 Z= 0.239 Angle : 0.636 9.905 13339 Z= 0.316 Chirality : 0.045 0.212 1451 Planarity : 0.005 0.059 1694 Dihedral : 6.116 59.226 1375 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.82 % Allowed : 22.24 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.38 (0.25), residues: 1151 helix: 0.50 (0.27), residues: 378 sheet: -0.46 (0.44), residues: 145 loop : -0.61 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 396 HIS 0.015 0.001 HIS B 88 PHE 0.050 0.002 PHE A 143 TYR 0.021 0.002 TYR B 582 ARG 0.014 0.001 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.66 seconds wall clock time: 75 minutes 26.54 seconds (4526.54 seconds total)