Starting phenix.real_space_refine on Tue Feb 13 11:39:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gaq_29904/02_2024/8gaq_29904.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3715 2.51 5 N 955 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E ASP 312": "OD1" <-> "OD2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E ARG 318": "NH1" <-> "NH2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E GLU 422": "OE1" <-> "OE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "G ARG 450": "NH1" <-> "NH2" Residue "G ARG 453": "NH1" <-> "NH2" Residue "G GLU 457": "OE1" <-> "OE2" Residue "G ASP 460": "OD1" <-> "OD2" Residue "G ARG 466": "NH1" <-> "NH2" Residue "G ARG 480": "NH1" <-> "NH2" Residue "G ARG 507": "NH1" <-> "NH2" Residue "G ARG 514": "NH1" <-> "NH2" Residue "G ASP 546": "OD1" <-> "OD2" Residue "G ARG 548": "NH1" <-> "NH2" Residue "G GLU 558": "OE1" <-> "OE2" Residue "G GLU 559": "OE1" <-> "OE2" Residue "G GLU 568": "OE1" <-> "OE2" Residue "G GLU 570": "OE1" <-> "OE2" Residue "G GLU 578": "OE1" <-> "OE2" Residue "G ARG 582": "NH1" <-> "NH2" Residue "G GLU 588": "OE1" <-> "OE2" Residue "I GLU 594": "OE1" <-> "OE2" Residue "I ARG 598": "NH1" <-> "NH2" Residue "I ARG 601": "NH1" <-> "NH2" Residue "I GLU 605": "OE1" <-> "OE2" Residue "I GLU 613": "OE1" <-> "OE2" Residue "I ARG 614": "NH1" <-> "NH2" Residue "I GLU 618": "OE1" <-> "OE2" Residue "I ARG 628": "NH1" <-> "NH2" Residue "I GLU 643": "OE1" <-> "OE2" Residue "I ARG 655": "NH1" <-> "NH2" Residue "I ARG 662": "NH1" <-> "NH2" Residue "I GLU 669": "OE1" <-> "OE2" Residue "I GLU 677": "OE1" <-> "OE2" Residue "I GLU 681": "OE1" <-> "OE2" Residue "I ASP 694": "OD1" <-> "OD2" Residue "I ARG 696": "NH1" <-> "NH2" Residue "I GLU 711": "OE1" <-> "OE2" Residue "I GLU 712": "OE1" <-> "OE2" Residue "I GLU 726": "OE1" <-> "OE2" Residue "I ARG 730": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5825 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "G" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "I" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Time building chain proxies: 3.57, per 1000 atoms: 0.61 Number of scatterers: 5825 At special positions: 0 Unit cell: (79.65, 76.995, 75.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1125 8.00 N 955 7.00 C 3715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 968.8 milliseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 91.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.544A pdb=" N LEU A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.759A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.737A pdb=" N VAL A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.590A pdb=" N LEU A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.166A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 4.008A pdb=" N GLU A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 134 removed outlier: 4.215A pdb=" N GLU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 164 through 182 removed outlier: 3.890A pdb=" N VAL C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.503A pdb=" N GLY C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.913A pdb=" N GLU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.867A pdb=" N LYS C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 255 Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.451A pdb=" N GLU C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 281 removed outlier: 4.294A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.539A pdb=" N ALA C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 289 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 Processing helix chain 'E' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 Processing helix chain 'E' and resid 346 through 362 removed outlier: 3.870A pdb=" N VAL E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 379 removed outlier: 3.630A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL E 369 " --> pdb=" O PRO E 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 395 removed outlier: 4.112A pdb=" N LYS E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 403 Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.138A pdb=" N GLU E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 430 removed outlier: 4.149A pdb=" N GLU E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.650A pdb=" N ALA E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 437 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 459 removed outlier: 3.790A pdb=" N GLU G 457 " --> pdb=" O ARG G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 477 removed outlier: 3.594A pdb=" N VAL G 477 " --> pdb=" O LEU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 480 No H-bonds generated for 'chain 'G' and resid 478 through 480' Processing helix chain 'G' and resid 481 through 492 Processing helix chain 'G' and resid 494 through 510 removed outlier: 3.876A pdb=" N VAL G 510 " --> pdb=" O LEU G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 527 removed outlier: 4.307A pdb=" N GLU G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 543 removed outlier: 4.202A pdb=" N LYS G 536 " --> pdb=" O LYS G 532 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 537 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 551 Processing helix chain 'G' and resid 552 through 560 removed outlier: 4.386A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 578 removed outlier: 4.036A pdb=" N GLU G 578 " --> pdb=" O ASP G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 590 Processing helix chain 'I' and resid 594 through 607 Processing helix chain 'I' and resid 608 through 626 removed outlier: 4.113A pdb=" N ARG I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 625 " --> pdb=" O LEU I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 640 removed outlier: 3.595A pdb=" N ASN I 635 " --> pdb=" O VAL I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 642 through 658 removed outlier: 3.889A pdb=" N VAL I 658 " --> pdb=" O LEU I 654 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 675 removed outlier: 3.992A pdb=" N GLU I 672 " --> pdb=" O LEU I 668 " (cutoff:3.500A) Processing helix chain 'I' and resid 678 through 691 removed outlier: 3.948A pdb=" N LYS I 684 " --> pdb=" O LYS I 680 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU I 688 " --> pdb=" O LYS I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 708 removed outlier: 4.055A pdb=" N LEU I 702 " --> pdb=" O LEU I 698 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 706 " --> pdb=" O LEU I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 710 through 726 removed outlier: 3.743A pdb=" N GLU I 719 " --> pdb=" O LYS I 715 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU I 726 " --> pdb=" O ASP I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 738 420 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 102 1.46 - 1.57: 3699 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 5845 Sorted by residual: bond pdb=" CB VAL G 553 " pdb=" CG1 VAL G 553 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB VAL I 701 " pdb=" CG1 VAL I 701 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CA ASP I 608 " pdb=" CB ASP I 608 " ideal model delta sigma weight residual 1.527 1.545 -0.017 1.61e-02 3.86e+03 1.18e+00 bond pdb=" CA ASP E 312 " pdb=" C ASP E 312 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.03e+00 bond pdb=" CB VAL C 257 " pdb=" CG1 VAL C 257 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 ... (remaining 5840 not shown) Histogram of bond angle deviations from ideal: 99.54 - 105.33: 91 105.33 - 111.13: 2344 111.13 - 116.92: 1705 116.92 - 122.72: 3434 122.72 - 128.51: 281 Bond angle restraints: 7855 Sorted by residual: angle pdb=" N VAL G 551 " pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 112.43 107.18 5.25 9.20e-01 1.18e+00 3.26e+01 angle pdb=" N LEU E 392 " pdb=" CA LEU E 392 " pdb=" C LEU E 392 " ideal model delta sigma weight residual 112.93 109.18 3.75 1.12e+00 7.97e-01 1.12e+01 angle pdb=" N LEU G 541 " pdb=" CA LEU G 541 " pdb=" C LEU G 541 " ideal model delta sigma weight residual 114.04 110.01 4.03 1.24e+00 6.50e-01 1.06e+01 angle pdb=" N LEU I 688 " pdb=" CA LEU I 688 " pdb=" C LEU I 688 " ideal model delta sigma weight residual 112.93 109.30 3.63 1.12e+00 7.97e-01 1.05e+01 angle pdb=" N LEU G 540 " pdb=" CA LEU G 540 " pdb=" C LEU G 540 " ideal model delta sigma weight residual 112.93 109.83 3.10 1.12e+00 7.97e-01 7.68e+00 ... (remaining 7850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3409 17.82 - 35.63: 276 35.63 - 53.45: 66 53.45 - 71.27: 31 71.27 - 89.09: 23 Dihedral angle restraints: 3805 sinusoidal: 1650 harmonic: 2155 Sorted by residual: dihedral pdb=" CA ASP I 694 " pdb=" C ASP I 694 " pdb=" N PRO I 695 " pdb=" CA PRO I 695 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP G 478 " pdb=" C ASP G 478 " pdb=" N PRO G 479 " pdb=" CA PRO G 479 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL C 255 " pdb=" C VAL C 255 " pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 648 0.034 - 0.068: 264 0.068 - 0.101: 52 0.101 - 0.135: 22 0.135 - 0.169: 4 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASP I 608 " pdb=" N ASP I 608 " pdb=" C ASP I 608 " pdb=" CB ASP I 608 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CB VAL A 101 " pdb=" CA VAL A 101 " pdb=" CG1 VAL A 101 " pdb=" CG2 VAL A 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB VAL E 397 " pdb=" CA VAL E 397 " pdb=" CG1 VAL E 397 " pdb=" CG2 VAL E 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 987 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 660 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO I 661 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO I 661 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 661 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 728 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO I 729 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 729 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 729 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 364 " -0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO E 365 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 365 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 365 " -0.025 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1286 2.80 - 3.33: 6254 3.33 - 3.85: 9017 3.85 - 4.38: 10624 4.38 - 4.90: 17742 Nonbonded interactions: 44923 Sorted by model distance: nonbonded pdb=" OE2 GLU G 465 " pdb=" ND2 ASN G 469 " model vdw 2.278 2.520 nonbonded pdb=" NH2 ARG G 582 " pdb=" OD2 ASP I 728 " model vdw 2.288 2.520 nonbonded pdb=" OD1 ASN A 43 " pdb=" N THR A 44 " model vdw 2.341 2.520 nonbonded pdb=" OD2 ASP A 136 " pdb=" NH2 ARG I 730 " model vdw 2.343 2.520 nonbonded pdb=" OD1 ASN G 487 " pdb=" N THR G 488 " model vdw 2.375 2.520 ... (remaining 44918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 9.240 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.360 Find NCS groups from input model: 0.370 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.005 0.037 5845 Z= 0.284 Angle : 0.701 6.872 7855 Z= 0.407 Chirality : 0.039 0.169 990 Planarity : 0.005 0.048 995 Dihedral : 16.745 89.085 2385 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.27), residues: 725 helix: -1.78 (0.18), residues: 625 sheet: None (None), residues: 0 loop : -2.52 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR G 498 ARG 0.007 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: C 173 ASN cc_start: 0.6646 (m-40) cc_final: 0.6295 (m110) REVERT: E 332 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7509 (ptp90) REVERT: I 622 LEU cc_start: 0.8737 (tp) cc_final: 0.8527 (tp) REVERT: I 628 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7599 (ptp90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2790 time to fit residues: 53.4571 Evaluate side-chains 107 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 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 93 ASN C 173 ASN E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5845 Z= 0.262 Angle : 0.628 6.960 7855 Z= 0.319 Chirality : 0.040 0.172 990 Planarity : 0.005 0.044 995 Dihedral : 4.664 16.994 775 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.22 % Allowed : 10.53 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), residues: 725 helix: -0.63 (0.19), residues: 639 sheet: None (None), residues: 0 loop : -1.34 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 54 ARG 0.009 0.001 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7533 (tptm) cc_final: 0.7189 (tptm) REVERT: E 332 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7483 (ptp90) REVERT: E 366 ARG cc_start: 0.7399 (ttm110) cc_final: 0.7168 (mtp-110) REVERT: E 417 MET cc_start: 0.6345 (tpp) cc_final: 0.4876 (ttm) REVERT: E 434 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: G 487 ASN cc_start: 0.7382 (p0) cc_final: 0.7173 (p0) REVERT: I 628 ARG cc_start: 0.8127 (ptt90) cc_final: 0.7368 (ptp90) outliers start: 8 outliers final: 3 residues processed: 119 average time/residue: 0.2773 time to fit residues: 39.9247 Evaluate side-chains 114 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain I residue 600 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.0070 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5845 Z= 0.153 Angle : 0.531 10.444 7855 Z= 0.266 Chirality : 0.037 0.173 990 Planarity : 0.003 0.032 995 Dihedral : 3.974 14.518 775 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.92 % Allowed : 12.67 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.31), residues: 725 helix: -0.00 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.06 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 54 ARG 0.005 0.000 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7461 (tptm) cc_final: 0.7144 (tptm) REVERT: E 417 MET cc_start: 0.6211 (tpp) cc_final: 0.4973 (ttm) REVERT: E 434 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7395 (ttm-80) REVERT: G 469 ASN cc_start: 0.7046 (t0) cc_final: 0.6774 (t0) REVERT: G 487 ASN cc_start: 0.7466 (p0) cc_final: 0.7265 (p0) outliers start: 6 outliers final: 3 residues processed: 134 average time/residue: 0.2505 time to fit residues: 41.0141 Evaluate side-chains 124 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain G residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5845 Z= 0.183 Angle : 0.546 7.616 7855 Z= 0.271 Chirality : 0.038 0.227 990 Planarity : 0.003 0.031 995 Dihedral : 3.900 14.540 775 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.75 % Allowed : 13.44 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 725 helix: 0.20 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.81 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 54 ARG 0.003 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7499 (tptm) cc_final: 0.7233 (tptm) REVERT: E 417 MET cc_start: 0.6480 (tpp) cc_final: 0.5022 (ttm) REVERT: E 434 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7337 (ttm-80) REVERT: G 487 ASN cc_start: 0.7513 (p0) cc_final: 0.7298 (p0) REVERT: I 645 MET cc_start: 0.5761 (ttt) cc_final: 0.5536 (ttt) REVERT: I 654 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8169 (tt) REVERT: I 688 LEU cc_start: 0.8395 (mp) cc_final: 0.8012 (tt) outliers start: 18 outliers final: 8 residues processed: 131 average time/residue: 0.2515 time to fit residues: 40.2300 Evaluate side-chains 125 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 600 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5845 Z= 0.244 Angle : 0.580 7.040 7855 Z= 0.290 Chirality : 0.039 0.230 990 Planarity : 0.003 0.035 995 Dihedral : 3.991 15.808 775 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.75 % Allowed : 13.44 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.32), residues: 725 helix: 0.20 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.58 (0.71), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 54 ARG 0.003 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (tt) REVERT: C 270 LYS cc_start: 0.7636 (tptm) cc_final: 0.7388 (tptm) REVERT: E 322 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 434 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: I 593 VAL cc_start: 0.6205 (m) cc_final: 0.5977 (m) REVERT: I 645 MET cc_start: 0.5850 (ttt) cc_final: 0.5643 (ttt) REVERT: I 654 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8223 (tt) REVERT: I 688 LEU cc_start: 0.8454 (mp) cc_final: 0.7932 (tt) REVERT: I 713 MET cc_start: 0.7178 (tpp) cc_final: 0.6839 (tpp) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.2560 time to fit residues: 40.8938 Evaluate side-chains 128 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 600 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5845 Z= 0.179 Angle : 0.549 7.075 7855 Z= 0.275 Chirality : 0.038 0.205 990 Planarity : 0.004 0.032 995 Dihedral : 3.769 14.777 775 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.29 % Allowed : 14.81 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.31), residues: 725 helix: 0.29 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.89 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR I 646 ARG 0.005 0.000 ARG I 598 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 269 MET cc_start: 0.7154 (tpp) cc_final: 0.6886 (tpt) REVERT: C 270 LYS cc_start: 0.7583 (tptm) cc_final: 0.7349 (tptm) REVERT: E 322 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 358 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (tt) REVERT: E 417 MET cc_start: 0.6549 (tpp) cc_final: 0.4849 (ttm) REVERT: I 593 VAL cc_start: 0.6205 (m) cc_final: 0.5975 (m) REVERT: I 654 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8188 (tt) REVERT: I 688 LEU cc_start: 0.8387 (mp) cc_final: 0.7906 (tt) REVERT: I 713 MET cc_start: 0.7111 (tpp) cc_final: 0.6699 (tpp) outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.2643 time to fit residues: 40.7245 Evaluate side-chains 124 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5845 Z= 0.198 Angle : 0.561 8.129 7855 Z= 0.280 Chirality : 0.038 0.183 990 Planarity : 0.004 0.032 995 Dihedral : 3.786 15.041 775 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.05 % Allowed : 14.20 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 725 helix: 0.31 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.94 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR I 646 ARG 0.009 0.000 ARG I 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 270 LYS cc_start: 0.7530 (tptm) cc_final: 0.7284 (tptm) REVERT: E 322 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8292 (mm-30) REVERT: I 593 VAL cc_start: 0.6000 (m) cc_final: 0.5787 (m) REVERT: I 654 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8199 (tt) REVERT: I 688 LEU cc_start: 0.8417 (mp) cc_final: 0.7898 (tt) outliers start: 20 outliers final: 15 residues processed: 124 average time/residue: 0.2458 time to fit residues: 37.6597 Evaluate side-chains 127 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN C 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5845 Z= 0.247 Angle : 0.627 9.659 7855 Z= 0.311 Chirality : 0.040 0.240 990 Planarity : 0.004 0.034 995 Dihedral : 3.917 15.868 775 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.90 % Allowed : 14.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 725 helix: 0.27 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.73 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR G 498 ARG 0.010 0.001 ARG I 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (tt) REVERT: C 270 LYS cc_start: 0.7466 (tptm) cc_final: 0.7221 (tptm) REVERT: I 593 VAL cc_start: 0.6043 (m) cc_final: 0.5822 (m) REVERT: I 654 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8244 (tt) REVERT: I 688 LEU cc_start: 0.8439 (mp) cc_final: 0.8046 (tt) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.2533 time to fit residues: 38.1888 Evaluate side-chains 125 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 458 ASP Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5845 Z= 0.215 Angle : 0.617 9.659 7855 Z= 0.306 Chirality : 0.039 0.238 990 Planarity : 0.004 0.034 995 Dihedral : 3.807 14.823 775 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.44 % Allowed : 16.34 % Favored : 81.22 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 725 helix: 0.31 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.70 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 498 ARG 0.010 0.000 ARG I 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.761 Fit side-chains REVERT: A 62 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8186 (tt) REVERT: E 366 ARG cc_start: 0.7026 (mtp-110) cc_final: 0.6801 (mtp-110) REVERT: E 417 MET cc_start: 0.6333 (tpp) cc_final: 0.4859 (mtt) REVERT: G 462 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7161 (tp30) REVERT: I 593 VAL cc_start: 0.5892 (m) cc_final: 0.5647 (m) REVERT: I 654 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8213 (tt) outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.2481 time to fit residues: 36.9309 Evaluate side-chains 125 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 458 ASP Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5845 Z= 0.203 Angle : 0.632 10.525 7855 Z= 0.308 Chirality : 0.038 0.229 990 Planarity : 0.004 0.038 995 Dihedral : 3.707 14.131 775 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.60 % Allowed : 15.88 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 725 helix: 0.36 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.87 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR G 498 ARG 0.009 0.001 ARG I 601 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.701 Fit side-chains REVERT: A 62 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8156 (tt) REVERT: C 270 LYS cc_start: 0.7596 (tptt) cc_final: 0.7216 (tppt) REVERT: E 366 ARG cc_start: 0.7025 (mtp-110) cc_final: 0.6808 (mtp-110) REVERT: G 462 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6957 (tp30) REVERT: I 593 VAL cc_start: 0.5680 (m) cc_final: 0.5463 (m) REVERT: I 654 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8225 (tt) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.2257 time to fit residues: 34.7924 Evaluate side-chains 125 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 458 ASP Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.0000 chunk 40 optimal weight: 0.0670 chunk 63 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.187983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155912 restraints weight = 7191.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158931 restraints weight = 4987.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.162315 restraints weight = 3568.852| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5845 Z= 0.193 Angle : 0.626 10.686 7855 Z= 0.307 Chirality : 0.039 0.225 990 Planarity : 0.004 0.048 995 Dihedral : 3.602 13.495 775 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.29 % Allowed : 16.34 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.31), residues: 725 helix: 0.40 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.80 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR G 498 ARG 0.009 0.001 ARG E 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.94 seconds wall clock time: 28 minutes 14.84 seconds (1694.84 seconds total)