Starting phenix.real_space_refine on Wed Feb 14 22:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/02_2024/7xqw_33402_updated.pdb" } resolution = 2.83 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= -0.004 sd= 0.416 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians W 1 12.54 5 Fe 20 7.16 5 P 5 5.49 5 S 85 5.16 5 C 6478 2.51 5 N 1847 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 547": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10391 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6070 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 46, 'TRANS': 743} Chain: "B" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4155 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 512} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' W': 1, 'FES': 1, 'MGD': 2, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2823 SG CYS A 436 38.796 41.161 97.901 1.00 30.06 S ATOM 265 SG CYS A 102 49.846 56.059 57.111 1.00 6.05 S ATOM 366 SG CYS A 115 50.188 58.413 56.214 1.00 5.19 S ATOM 388 SG CYS A 118 54.459 56.843 55.167 1.00 6.36 S ATOM 490 SG CYS A 132 53.154 54.080 57.928 1.00 6.68 S ATOM 1137 SG CYS A 216 44.284 58.289 60.773 1.00 5.04 S ATOM 1114 SG CYS A 213 37.999 59.406 59.077 1.00 4.73 S ATOM 1497 SG CYS A 266 41.040 61.341 64.716 1.00 4.47 S ATOM 1159 SG CYS A 219 39.339 55.080 63.198 1.00 4.82 S ATOM 1470 SG CYS A 262 38.075 55.629 69.657 1.00 4.49 S ATOM 1433 SG CYS A 256 33.221 53.159 72.467 1.00 7.86 S ATOM 1451 SG CYS A 259 39.131 51.450 74.442 1.00 4.94 S ATOM 1188 SG CYS A 223 37.224 49.225 68.875 1.00 5.66 S ATOM 1718 SG CYS A 295 42.563 54.021 86.838 1.00 10.97 S ATOM 1977 SG CYS A 329 39.198 50.941 82.741 1.00 6.79 S ATOM 1743 SG CYS A 298 40.939 48.104 86.685 1.00 11.58 S ATOM 1764 SG CYS A 302 45.768 51.518 82.517 1.00 10.15 S ATOM 10068 SG CYS B 542 45.532 49.480 43.520 1.00 6.26 S ATOM 9808 SG CYS B 508 42.415 54.946 43.829 1.00 5.94 S ATOM 9788 SG CYS B 505 46.218 54.628 47.560 1.00 5.57 S ATOM 9769 SG CYS B 502 41.464 49.903 48.254 1.00 5.50 S ATOM 6791 SG CYS B 113 28.519 49.098 31.049 1.00 15.72 S ATOM 6826 SG CYS B 118 27.173 48.927 27.718 1.00 16.89 S ATOM 7038 SG CYS B 146 32.281 46.333 30.942 1.00 13.72 S ATOM 7063 SG CYS B 150 32.668 46.254 27.160 1.00 17.32 S Time building chain proxies: 6.23, per 1000 atoms: 0.60 Number of scatterers: 10391 At special positions: 0 Unit cell: (85.32, 86.4, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 85 16.00 P 5 15.00 O 1955 8.00 N 1847 7.00 C 6478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 102 " pdb="FE1 FES A1004 " - pdb=" N HIS A 103 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 118 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 132 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 115 " pdb=" FES B 603 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 113 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 150 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 118 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 146 " pdb=" SF4 A1005 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 216 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 219 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 213 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 266 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 256 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 259 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 223 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 262 " pdb=" SF4 A1007 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 295 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 329 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 298 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 302 " pdb=" SF4 B 602 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 505 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 542 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 502 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 508 " Number of angles added : 62 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 9 sheets defined 37.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 147 through 163 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 379 through 394 removed outlier: 3.583A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.589A pdb=" N ARG A 507 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 539 through 545 removed outlier: 4.387A pdb=" N GLY A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.849A pdb=" N ARG A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 4.422A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 594 through 597 No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 657 through 667 Processing helix chain 'A' and resid 679 through 688 removed outlier: 3.803A pdb=" N HIS A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 730 through 733 No H-bonds generated for 'chain 'A' and resid 730 through 733' Processing helix chain 'A' and resid 774 through 785 Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'A' and resid 813 through 817 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 62 removed outlier: 4.958A pdb=" N ILE B 53 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.642A pdb=" N ALA B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.594A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 506 through 519 removed outlier: 3.994A pdb=" N GLN B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 550 through 558 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing sheet with id= A, first strand: chain 'A' and resid 206 through 208 Processing sheet with id= B, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.698A pdb=" N TYR A 315 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 349 through 351 Processing sheet with id= D, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= E, first strand: chain 'A' and resid 494 through 496 removed outlier: 6.563A pdb=" N GLY A 625 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N TRP A 592 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS A 627 " --> pdb=" O TRP A 592 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 749 through 752 Processing sheet with id= G, first strand: chain 'B' and resid 139 through 144 removed outlier: 6.795A pdb=" N LEU B 108 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 142 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 110 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B 144 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 112 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 365 through 369 removed outlier: 7.202A pdb=" N LEU B 249 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ASN B 368 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 251 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 250 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 319 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE B 293 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 295 " --> pdb=" O HIS B 321 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG B 323 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 411 through 416 303 hydrogen bonds defined for protein. 852 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: 3.26 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4448 1.43 - 1.64: 6039 1.64 - 1.86: 99 1.86 - 2.07: 2 2.07 - 2.28: 56 Bond restraints: 10644 Sorted by residual: bond pdb=" C12 MGD A1002 " pdb=" C13 MGD A1002 " ideal model delta sigma weight residual 1.337 1.526 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C6 MGD A1002 " pdb=" O6 MGD A1002 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" C6 MGD A1003 " pdb=" O6 MGD A1003 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C12 MGD A1003 " pdb=" C13 MGD A1003 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C17 MGD A1002 " pdb=" O17 MGD A1002 " ideal model delta sigma weight residual 1.232 1.398 -0.166 2.00e-02 2.50e+03 6.87e+01 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 73.43 - 85.77: 52 85.77 - 98.12: 0 98.12 - 110.47: 2958 110.47 - 122.81: 10492 122.81 - 135.16: 1009 Bond angle restraints: 14511 Sorted by residual: angle pdb=" C13 MGD A1003 " pdb=" C12 MGD A1003 " pdb=" S12 MGD A1003 " ideal model delta sigma weight residual 125.54 108.41 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3A MGD A1003 " pdb=" PA MGD A1003 " pdb=" O3B MGD A1003 " ideal model delta sigma weight residual 93.37 109.82 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3B MGD A1002 " pdb=" PB MGD A1002 " pdb=" O5' MGD A1002 " ideal model delta sigma weight residual 93.25 108.57 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C13 MGD A1002 " pdb=" C12 MGD A1002 " pdb=" S12 MGD A1002 " ideal model delta sigma weight residual 125.54 110.48 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O3A MGD A1002 " pdb=" PA MGD A1002 " pdb=" O3B MGD A1002 " ideal model delta sigma weight residual 93.37 108.03 -14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 6216 32.85 - 65.71: 162 65.71 - 98.56: 19 98.56 - 131.41: 1 131.41 - 164.26: 2 Dihedral angle restraints: 6400 sinusoidal: 2604 harmonic: 3796 Sorted by residual: dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 93.33 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" CA LYS B 351 " pdb=" C LYS B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" O5' MGD A1003 " pdb=" O3B MGD A1003 " pdb=" PB MGD A1003 " pdb=" PA MGD A1003 " ideal model delta sinusoidal sigma weight residual 203.73 43.28 160.45 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 6397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1479 0.087 - 0.174: 106 0.174 - 0.261: 4 0.261 - 0.348: 1 0.348 - 0.435: 3 Chirality restraints: 1593 Sorted by residual: chirality pdb=" C4' MGD A1003 " pdb=" C3' MGD A1003 " pdb=" C5' MGD A1003 " pdb=" O4' MGD A1003 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA ALA A 711 " pdb=" N ALA A 711 " pdb=" C ALA A 711 " pdb=" CB ALA A 711 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA GLU A 835 " pdb=" N GLU A 835 " pdb=" C GLU A 835 " pdb=" CB GLU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1590 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " 0.067 2.00e-02 2.50e+03 1.23e-01 4.14e+02 pdb=" C17 MGD A1002 " -0.008 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " -0.021 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " 0.094 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " -0.311 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " 0.110 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " -0.051 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " -0.067 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " 0.053 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " 0.176 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' MGD A1003 " -0.093 2.00e-02 2.50e+03 3.53e-02 3.73e+01 pdb=" C2 MGD A1003 " 0.007 2.00e-02 2.50e+03 pdb=" C4 MGD A1003 " 0.026 2.00e-02 2.50e+03 pdb=" C5 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" C6 MGD A1003 " -0.016 2.00e-02 2.50e+03 pdb=" C8 MGD A1003 " 0.034 2.00e-02 2.50e+03 pdb=" N1 MGD A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N2 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N3 MGD A1003 " 0.025 2.00e-02 2.50e+03 pdb=" N7 MGD A1003 " 0.011 2.00e-02 2.50e+03 pdb=" N9 MGD A1003 " 0.043 2.00e-02 2.50e+03 pdb=" O6 MGD A1003 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 351 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 352 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 352 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 352 " 0.032 5.00e-02 4.00e+02 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 46 2.44 - 3.06: 7231 3.06 - 3.67: 16310 3.67 - 4.29: 25784 4.29 - 4.90: 41625 Nonbonded interactions: 90996 Sorted by model distance: nonbonded pdb=" OD2 ASP A 725 " pdb=" CG2 THR A 729 " model vdw 1.827 3.460 nonbonded pdb=" O2' FMN B 601 " pdb=" O4' FMN B 601 " model vdw 1.898 2.440 nonbonded pdb=" OD1 ASP A 725 " pdb=" N LEU A 726 " model vdw 2.154 2.520 nonbonded pdb=" OE1 GLN A 325 " pdb=" NH2 ARG A 327 " model vdw 2.204 2.520 nonbonded pdb=" O VAL A 479 " pdb=" OG1 THR A 482 " model vdw 2.211 2.440 ... (remaining 90991 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.620 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.490 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.007 0.189 10644 Z= 0.479 Angle : 0.792 17.134 14511 Z= 0.350 Chirality : 0.047 0.435 1593 Planarity : 0.006 0.123 1896 Dihedral : 15.553 164.263 3968 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.75 (0.23), residues: 1327 helix: 0.50 (0.24), residues: 503 sheet: -0.08 (0.54), residues: 100 loop : -1.30 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 524 HIS 0.011 0.001 HIS B 57 PHE 0.013 0.001 PHE A 245 TYR 0.021 0.001 TYR A 824 ARG 0.009 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.114 Fit side-chains REVERT: A 389 LYS cc_start: 0.7553 (tttm) cc_final: 0.7256 (tttt) REVERT: A 555 LYS cc_start: 0.7266 (ttpt) cc_final: 0.7017 (mtmp) REVERT: A 730 GLU cc_start: 0.7358 (mp0) cc_final: 0.7019 (mp0) REVERT: B 44 THR cc_start: 0.8119 (p) cc_final: 0.7892 (t) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 1.2472 time to fit residues: 250.8860 Evaluate side-chains 122 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 164 GLN A 217 ASN A 428 ASN A 669 GLN A 724 GLN A 810 ASN B 273 HIS B 492 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10644 Z= 0.233 Angle : 0.632 10.687 14511 Z= 0.305 Chirality : 0.046 0.187 1593 Planarity : 0.005 0.073 1896 Dihedral : 10.306 159.204 1589 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.81 % Allowed : 11.52 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.75 (0.23), residues: 1327 helix: 0.35 (0.22), residues: 518 sheet: -0.25 (0.48), residues: 117 loop : -1.20 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 524 HIS 0.010 0.001 HIS A 713 PHE 0.013 0.002 PHE A 245 TYR 0.020 0.002 TYR A 824 ARG 0.007 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.131 Fit side-chains REVERT: A 389 LYS cc_start: 0.7453 (tttm) cc_final: 0.7103 (tttt) REVERT: A 437 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6522 (m-70) REVERT: A 490 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 589 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 730 GLU cc_start: 0.7719 (mp0) cc_final: 0.7353 (mp0) REVERT: A 827 ASP cc_start: 0.5402 (OUTLIER) cc_final: 0.5128 (m-30) REVERT: B 44 THR cc_start: 0.8098 (p) cc_final: 0.7884 (t) outliers start: 30 outliers final: 12 residues processed: 159 average time/residue: 1.1866 time to fit residues: 204.7220 Evaluate side-chains 135 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 431 HIS A 598 GLN A 720 HIS A 724 GLN A 734 HIS A 810 ASN B 483 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 10644 Z= 0.512 Angle : 0.807 15.323 14511 Z= 0.392 Chirality : 0.053 0.242 1593 Planarity : 0.006 0.077 1896 Dihedral : 10.503 164.203 1589 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.78 % Allowed : 13.48 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1327 helix: -0.44 (0.22), residues: 523 sheet: -0.51 (0.46), residues: 127 loop : -1.48 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 524 HIS 0.007 0.002 HIS A 431 PHE 0.024 0.003 PHE A 245 TYR 0.032 0.003 TYR A 824 ARG 0.008 0.001 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 1.219 Fit side-chains REVERT: A 490 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 491 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6199 (mmm-85) REVERT: A 589 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8003 (tt) REVERT: A 630 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6480 (mtt-85) REVERT: A 730 GLU cc_start: 0.7930 (mp0) cc_final: 0.7521 (mp0) REVERT: B 44 THR cc_start: 0.8242 (p) cc_final: 0.8029 (t) REVERT: B 65 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: B 333 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7789 (tm-30) outliers start: 51 outliers final: 28 residues processed: 156 average time/residue: 1.2865 time to fit residues: 216.4226 Evaluate side-chains 144 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 810 ASN B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10644 Z= 0.197 Angle : 0.592 11.403 14511 Z= 0.286 Chirality : 0.044 0.188 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.870 158.520 1589 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.68 % Allowed : 15.36 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1327 helix: 0.06 (0.23), residues: 511 sheet: -0.38 (0.48), residues: 117 loop : -1.31 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 524 HIS 0.004 0.001 HIS A 431 PHE 0.015 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.008 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 1.291 Fit side-chains REVERT: A 490 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: A 589 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 650 ASP cc_start: 0.7597 (t0) cc_final: 0.7150 (t0) REVERT: A 730 GLU cc_start: 0.7828 (mp0) cc_final: 0.7513 (mp0) REVERT: B 61 ASP cc_start: 0.7639 (m-30) cc_final: 0.7186 (m-30) REVERT: B 65 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: B 102 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.4847 (mp0) REVERT: B 319 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6740 (ptt90) REVERT: B 333 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7327 (tm-30) outliers start: 50 outliers final: 23 residues processed: 167 average time/residue: 1.2420 time to fit residues: 223.3359 Evaluate side-chains 148 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 724 GLN A 810 ASN B 368 ASN B 521 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10644 Z= 0.353 Angle : 0.690 13.606 14511 Z= 0.332 Chirality : 0.048 0.210 1593 Planarity : 0.005 0.077 1896 Dihedral : 10.020 161.540 1589 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.34 % Allowed : 16.95 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1327 helix: -0.15 (0.22), residues: 518 sheet: -0.49 (0.45), residues: 125 loop : -1.46 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 524 HIS 0.004 0.001 HIS A 431 PHE 0.020 0.002 PHE A 245 TYR 0.024 0.002 TYR A 824 ARG 0.007 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 119 time to evaluate : 1.247 Fit side-chains REVERT: A 490 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: A 491 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6254 (mmm-85) REVERT: A 589 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8038 (tt) REVERT: A 630 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6562 (mtt-85) REVERT: A 650 ASP cc_start: 0.7645 (t0) cc_final: 0.7274 (t0) REVERT: A 730 GLU cc_start: 0.7932 (mp0) cc_final: 0.7582 (mp0) REVERT: B 61 ASP cc_start: 0.7690 (m-30) cc_final: 0.7222 (m-30) REVERT: B 65 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: B 102 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.4970 (mp0) REVERT: B 139 VAL cc_start: 0.7569 (OUTLIER) cc_final: 0.7271 (t) REVERT: B 333 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7444 (tm-30) outliers start: 57 outliers final: 31 residues processed: 159 average time/residue: 1.2661 time to fit residues: 216.9150 Evaluate side-chains 154 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN A 810 ASN B 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10644 Z= 0.263 Angle : 0.626 12.216 14511 Z= 0.302 Chirality : 0.045 0.196 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.870 159.746 1589 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.15 % Allowed : 16.85 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1327 helix: -0.03 (0.22), residues: 516 sheet: -0.51 (0.46), residues: 117 loop : -1.43 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 524 HIS 0.005 0.001 HIS A 431 PHE 0.016 0.002 PHE A 245 TYR 0.020 0.002 TYR A 824 ARG 0.008 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 120 time to evaluate : 1.301 Fit side-chains REVERT: A 490 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: A 491 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6288 (mmm-85) REVERT: A 589 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 630 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6500 (mtt-85) REVERT: A 650 ASP cc_start: 0.7323 (t0) cc_final: 0.7053 (t0) REVERT: A 730 GLU cc_start: 0.7946 (mp0) cc_final: 0.7652 (mp0) REVERT: B 61 ASP cc_start: 0.7676 (m-30) cc_final: 0.7252 (m-30) REVERT: B 65 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: B 87 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 102 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.4741 (mp0) REVERT: B 333 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7348 (tm-30) outliers start: 55 outliers final: 34 residues processed: 161 average time/residue: 1.2629 time to fit residues: 220.4077 Evaluate side-chains 153 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN A 810 ASN B 483 GLN B 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10644 Z= 0.223 Angle : 0.594 11.482 14511 Z= 0.287 Chirality : 0.044 0.182 1593 Planarity : 0.005 0.076 1896 Dihedral : 9.699 158.771 1589 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.78 % Allowed : 17.79 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1327 helix: 0.15 (0.23), residues: 509 sheet: -0.49 (0.47), residues: 117 loop : -1.37 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 524 HIS 0.004 0.001 HIS A 431 PHE 0.016 0.001 PHE A 245 TYR 0.018 0.001 TYR A 824 ARG 0.008 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 1.279 Fit side-chains REVERT: A 490 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: A 491 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6279 (mmm-85) REVERT: A 589 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 640 ASP cc_start: 0.7824 (m-30) cc_final: 0.7621 (m-30) REVERT: A 650 ASP cc_start: 0.7261 (t0) cc_final: 0.7029 (t0) REVERT: A 730 GLU cc_start: 0.7928 (mp0) cc_final: 0.7697 (mp0) REVERT: A 850 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7287 (ttpp) REVERT: B 61 ASP cc_start: 0.7629 (m-30) cc_final: 0.7091 (m-30) REVERT: B 87 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: B 102 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.4646 (mp0) REVERT: B 333 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7307 (tm-30) outliers start: 51 outliers final: 34 residues processed: 159 average time/residue: 1.2454 time to fit residues: 213.7319 Evaluate side-chains 154 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 554 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.174 Angle : 0.557 11.309 14511 Z= 0.269 Chirality : 0.043 0.170 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.513 157.822 1589 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.03 % Allowed : 18.54 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.86 (0.23), residues: 1327 helix: 0.35 (0.23), residues: 507 sheet: -0.48 (0.47), residues: 117 loop : -1.28 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 592 HIS 0.004 0.001 HIS A 431 PHE 0.014 0.001 PHE A 245 TYR 0.015 0.001 TYR B 92 ARG 0.009 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.228 Fit side-chains REVERT: A 490 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: A 491 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6221 (mmm-85) REVERT: A 630 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6451 (mtt-85) REVERT: A 640 ASP cc_start: 0.7710 (m-30) cc_final: 0.7462 (m-30) REVERT: A 648 TYR cc_start: 0.7779 (m-80) cc_final: 0.7570 (m-80) REVERT: A 650 ASP cc_start: 0.7252 (t0) cc_final: 0.6964 (t0) REVERT: B 61 ASP cc_start: 0.7391 (m-30) cc_final: 0.6868 (m-30) REVERT: B 87 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: B 102 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.4730 (mp0) REVERT: B 319 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6743 (ptt90) outliers start: 43 outliers final: 27 residues processed: 158 average time/residue: 1.4031 time to fit residues: 237.8005 Evaluate side-chains 146 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 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 724 GLN A 810 ASN B 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10644 Z= 0.223 Angle : 0.589 11.490 14511 Z= 0.284 Chirality : 0.044 0.182 1593 Planarity : 0.005 0.076 1896 Dihedral : 9.556 158.581 1589 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.21 % Allowed : 18.73 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.90 (0.23), residues: 1327 helix: 0.28 (0.23), residues: 509 sheet: -0.48 (0.47), residues: 117 loop : -1.29 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 524 HIS 0.005 0.001 HIS A 437 PHE 0.014 0.001 PHE A 245 TYR 0.018 0.001 TYR A 824 ARG 0.008 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 1.192 Fit side-chains REVERT: A 490 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: A 491 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6257 (mmm-85) REVERT: A 630 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6507 (mtt-85) REVERT: A 648 TYR cc_start: 0.7691 (m-80) cc_final: 0.7488 (m-80) REVERT: A 650 ASP cc_start: 0.7310 (t0) cc_final: 0.7036 (t0) REVERT: B 61 ASP cc_start: 0.7447 (m-30) cc_final: 0.6876 (m-30) REVERT: B 87 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: B 102 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.4928 (mp0) REVERT: B 319 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6909 (ptt90) outliers start: 45 outliers final: 30 residues processed: 149 average time/residue: 1.2470 time to fit residues: 200.5088 Evaluate side-chains 143 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10644 Z= 0.310 Angle : 0.656 12.690 14511 Z= 0.318 Chirality : 0.047 0.205 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.779 160.981 1589 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.21 % Allowed : 19.19 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1327 helix: 0.03 (0.22), residues: 516 sheet: -0.55 (0.47), residues: 117 loop : -1.38 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 524 HIS 0.007 0.001 HIS A 437 PHE 0.015 0.002 PHE A 245 TYR 0.023 0.002 TYR A 824 ARG 0.009 0.001 ARG B 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 1.180 Fit side-chains REVERT: A 490 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: A 491 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6212 (mmm-85) REVERT: A 630 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6478 (mtt-85) REVERT: A 648 TYR cc_start: 0.7798 (m-80) cc_final: 0.7590 (m-80) REVERT: A 650 ASP cc_start: 0.7321 (t0) cc_final: 0.7043 (t0) REVERT: A 717 MET cc_start: 0.7359 (ttp) cc_final: 0.7089 (tpp) REVERT: B 61 ASP cc_start: 0.7732 (m-30) cc_final: 0.7213 (m-30) REVERT: B 102 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.4922 (mp0) REVERT: B 139 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7237 (t) outliers start: 45 outliers final: 30 residues processed: 153 average time/residue: 1.2730 time to fit residues: 210.7401 Evaluate side-chains 147 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 92 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 810 ASN B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122284 restraints weight = 6034.976| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.98 r_work: 0.3348 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10644 Z= 0.273 Angle : 0.634 12.202 14511 Z= 0.305 Chirality : 0.045 0.194 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.729 159.967 1589 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.03 % Allowed : 19.19 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1327 helix: 0.04 (0.23), residues: 516 sheet: -0.60 (0.46), residues: 117 loop : -1.41 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 524 HIS 0.006 0.001 HIS A 437 PHE 0.015 0.002 PHE A 245 TYR 0.021 0.002 TYR A 824 ARG 0.009 0.001 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.79 seconds wall clock time: 73 minutes 7.16 seconds (4387.16 seconds total)