Starting phenix.real_space_refine on Sat Dec 9 03:08:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcz_21618/12_2023/6wcz_21618.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 C 6251 2.51 5 N 1776 2.21 5 O 1809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2829 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 7065 Unusual residues: {' ZN': 2} Classifications: {'peptide': 881, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 848, None: 2} Not linked: pdbres="LEU B 886 " pdbres=" ZN B1001 " Not linked: pdbres=" ZN B1001 " pdbres=" ZN B1002 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6330 SG CYS B 448 58.566 50.765 29.088 1.00170.38 S ATOM 6352 SG CYS B 451 56.478 53.324 30.558 1.00177.22 S ATOM 9587 SG CYS B 849 21.281 71.420 51.638 1.00143.74 S Time building chain proxies: 5.83, per 1000 atoms: 0.59 Number of scatterers: 9894 At special positions: 0 Unit cell: (82.39, 105.93, 157.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 56 16.00 O 1809 8.00 N 1776 7.00 C 6251 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: 3.91 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 443 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 451 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 448 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 714 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 849 " 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 47.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 140 through 182 removed outlier: 3.669A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 243 removed outlier: 3.802A pdb=" N ARG A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 256 through 277 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.819A pdb=" N GLY A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.771A pdb=" N GLU A 426 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.109A pdb=" N ILE A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 11 through 19 removed outlier: 4.316A pdb=" N ASN B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.792A pdb=" N PHE B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 47 removed outlier: 4.536A pdb=" N LYS B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.931A pdb=" N THR B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.826A pdb=" N HIS B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET B 135 " --> pdb=" O VAL B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 153 through 172 removed outlier: 4.123A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 removed outlier: 4.251A pdb=" N ARG B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.810A pdb=" N ILE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.663A pdb=" N ARG B 327 " --> pdb=" O ASN B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.957A pdb=" N ARG B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.908A pdb=" N SER B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 430 through 446 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.564A pdb=" N ILE B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.870A pdb=" N ILE B 543 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.793A pdb=" N LEU B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.660A pdb=" N LEU B 553 " --> pdb=" O ASN B 550 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 554 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 558 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 607 through 628 removed outlier: 3.617A pdb=" N LEU B 611 " --> pdb=" O VAL B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 658 removed outlier: 4.152A pdb=" N VAL B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TRP B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.748A pdb=" N ALA B 677 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 750 through 767 Processing helix chain 'B' and resid 772 through 785 removed outlier: 3.584A pdb=" N LEU B 776 " --> pdb=" O ARG B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 807 removed outlier: 3.901A pdb=" N MET B 806 " --> pdb=" O GLY B 803 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 807 " --> pdb=" O GLU B 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 803 through 807' Processing helix chain 'B' and resid 810 through 820 removed outlier: 3.706A pdb=" N VAL B 814 " --> pdb=" O ASP B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 855 through 862 Processing helix chain 'B' and resid 865 through 876 removed outlier: 3.831A pdb=" N VAL B 872 " --> pdb=" O THR B 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 removed outlier: 5.874A pdb=" N VAL A 318 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG A 345 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 343 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.198A pdb=" N THR A 358 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS A 436 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127 removed outlier: 8.596A pdb=" N ARG B 125 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 100 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS B 127 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 102 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY B 75 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL B 100 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 77 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLY B 102 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 79 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 143 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LYS B 182 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N CYS B 145 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 207 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 305 through 310 removed outlier: 3.514A pdb=" N HIS B 307 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 594 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER B 309 " --> pdb=" O MET B 592 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET B 592 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457 Processing sheet with id=AA8, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AA9, first strand: chain 'B' and resid 714 through 718 404 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2401 1.33 - 1.45: 2089 1.45 - 1.57: 5527 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 10109 Sorted by residual: bond pdb=" N ARG B 42 " pdb=" CA ARG B 42 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N GLY B 107 " pdb=" CA GLY B 107 " ideal model delta sigma weight residual 1.443 1.477 -0.034 1.37e-02 5.33e+03 6.21e+00 bond pdb=" N GLN A 141 " pdb=" CA GLN A 141 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.55e+00 bond pdb=" CB TRP B 498 " pdb=" CG TRP B 498 " ideal model delta sigma weight residual 1.498 1.426 0.072 3.10e-02 1.04e+03 5.47e+00 bond pdb=" CB THR B 263 " pdb=" CG2 THR B 263 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.31e+00 ... (remaining 10104 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.42: 124 103.42 - 111.11: 3709 111.11 - 118.80: 4406 118.80 - 126.49: 5213 126.49 - 134.18: 210 Bond angle restraints: 13662 Sorted by residual: angle pdb=" N VAL B 132 " pdb=" CA VAL B 132 " pdb=" CB VAL B 132 " ideal model delta sigma weight residual 112.39 105.29 7.10 1.17e+00 7.31e-01 3.68e+01 angle pdb=" C LEU A 307 " pdb=" N LEU A 308 " pdb=" CA LEU A 308 " ideal model delta sigma weight residual 121.14 113.38 7.76 1.75e+00 3.27e-01 1.97e+01 angle pdb=" CG ARG A 300 " pdb=" CD ARG A 300 " pdb=" NE ARG A 300 " ideal model delta sigma weight residual 112.00 121.48 -9.48 2.20e+00 2.07e-01 1.86e+01 angle pdb=" C ARG B 681 " pdb=" N PHE B 682 " pdb=" CA PHE B 682 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 109.81 118.81 -9.00 2.21e+00 2.05e-01 1.66e+01 ... (remaining 13657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5545 16.81 - 33.63: 432 33.63 - 50.44: 87 50.44 - 67.26: 8 67.26 - 84.07: 4 Dihedral angle restraints: 6076 sinusoidal: 2539 harmonic: 3537 Sorted by residual: dihedral pdb=" CA ASN B 407 " pdb=" C ASN B 407 " pdb=" N ALA B 408 " pdb=" CA ALA B 408 " ideal model delta harmonic sigma weight residual -180.00 -135.58 -44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA LYS A 375 " pdb=" C LYS A 375 " pdb=" N PHE A 376 " pdb=" CA PHE A 376 " ideal model delta harmonic sigma weight residual 180.00 144.33 35.67 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ILE B 278 " pdb=" C ILE B 278 " pdb=" N GLY B 279 " pdb=" CA GLY B 279 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 ... (remaining 6073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 875 0.050 - 0.100: 427 0.100 - 0.150: 135 0.150 - 0.199: 30 0.199 - 0.249: 7 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CG LEU B 435 " pdb=" CB LEU B 435 " pdb=" CD1 LEU B 435 " pdb=" CD2 LEU B 435 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 431 " pdb=" CA ILE A 431 " pdb=" CG1 ILE A 431 " pdb=" CG2 ILE A 431 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE A 363 " pdb=" CA ILE A 363 " pdb=" CG1 ILE A 363 " pdb=" CG2 ILE A 363 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1471 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 107 " 0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO B 108 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 42 " -0.239 9.50e-02 1.11e+02 1.07e-01 7.01e+00 pdb=" NE ARG B 42 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 42 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 42 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 42 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 497 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 498 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.035 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.21: 9063 3.21 - 3.77: 16102 3.77 - 4.34: 20515 4.34 - 4.90: 31925 Nonbonded interactions: 77860 Sorted by model distance: nonbonded pdb=" OE2 GLU B 439 " pdb="ZN ZN B1001 " model vdw 2.085 2.230 nonbonded pdb=" O ARG B 41 " pdb=" NE ARG B 42 " model vdw 2.115 2.520 nonbonded pdb=" O LEU B 611 " pdb=" OG1 THR B 615 " model vdw 2.201 2.440 nonbonded pdb=" O MET B 375 " pdb=" OG SER B 379 " model vdw 2.228 2.440 nonbonded pdb=" O GLU A 259 " pdb=" OG1 THR A 263 " model vdw 2.236 2.440 ... (remaining 77855 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=0.87 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: 1.040 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: 4.190 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.009 0.072 10109 Z= 0.594 Angle : 1.216 9.485 13662 Z= 0.659 Chirality : 0.064 0.249 1474 Planarity : 0.009 0.107 1749 Dihedral : 12.526 84.069 3798 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 2.55 % Allowed : 8.40 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -4.79 (0.18), residues: 1221 helix: -3.20 (0.15), residues: 510 sheet: -2.21 (0.47), residues: 93 loop : -3.34 (0.21), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP A 238 HIS 0.011 0.003 HIS A 271 PHE 0.025 0.005 PHE B 432 TYR 0.031 0.004 TYR B 882 ARG 0.015 0.002 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 194 average time/residue: 0.3206 time to fit residues: 80.1848 Evaluate side-chains 110 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.239 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1463 time to fit residues: 4.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 313 HIS A 461 GLN A 473 ASN A 480 GLN B 228 ASN B 402 ASN ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10109 Z= 0.213 Angle : 0.725 7.526 13662 Z= 0.381 Chirality : 0.043 0.168 1474 Planarity : 0.006 0.062 1749 Dihedral : 6.607 32.445 1350 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.02 % Allowed : 13.41 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.21), residues: 1221 helix: -1.30 (0.21), residues: 506 sheet: -1.61 (0.51), residues: 91 loop : -2.89 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 476 HIS 0.013 0.001 HIS A 313 PHE 0.025 0.002 PHE A 504 TYR 0.026 0.002 TYR A 288 ARG 0.006 0.001 ARG B 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 140 average time/residue: 0.2449 time to fit residues: 47.5642 Evaluate side-chains 111 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.120 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1042 time to fit residues: 4.4941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 HIS B 550 ASN B 598 GLN ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN B 652 ASN ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10109 Z= 0.171 Angle : 0.658 9.211 13662 Z= 0.334 Chirality : 0.041 0.158 1474 Planarity : 0.005 0.060 1749 Dihedral : 5.726 28.421 1350 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.02 % Allowed : 15.20 % Favored : 81.78 % 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: -2.49 (0.23), residues: 1221 helix: -0.55 (0.22), residues: 516 sheet: -1.67 (0.50), residues: 100 loop : -2.71 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 848 HIS 0.003 0.001 HIS B 678 PHE 0.028 0.002 PHE A 504 TYR 0.019 0.001 TYR A 288 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 154 average time/residue: 0.2141 time to fit residues: 47.0521 Evaluate side-chains 113 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.132 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1041 time to fit residues: 3.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 ASN ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10109 Z= 0.162 Angle : 0.662 13.372 13662 Z= 0.327 Chirality : 0.042 0.172 1474 Planarity : 0.004 0.060 1749 Dihedral : 5.376 25.076 1350 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.46 % Allowed : 17.66 % Favored : 79.89 % 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: -2.09 (0.23), residues: 1221 helix: -0.13 (0.22), residues: 522 sheet: -1.34 (0.53), residues: 96 loop : -2.63 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 539 HIS 0.004 0.001 HIS B 217 PHE 0.028 0.002 PHE A 504 TYR 0.020 0.001 TYR A 288 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 26 outliers final: 13 residues processed: 141 average time/residue: 0.2279 time to fit residues: 45.5404 Evaluate side-chains 119 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.309 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.1476 time to fit residues: 4.7405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.0020 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10109 Z= 0.174 Angle : 0.673 10.272 13662 Z= 0.329 Chirality : 0.043 0.190 1474 Planarity : 0.004 0.059 1749 Dihedral : 5.196 21.875 1350 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.17 % Allowed : 19.55 % Favored : 78.28 % 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: -1.93 (0.23), residues: 1221 helix: -0.01 (0.23), residues: 522 sheet: -1.55 (0.51), residues: 101 loop : -2.46 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 539 HIS 0.004 0.001 HIS B 217 PHE 0.025 0.002 PHE A 504 TYR 0.015 0.001 TYR A 402 ARG 0.005 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.2168 time to fit residues: 41.1857 Evaluate side-chains 114 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.142 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1001 time to fit residues: 3.7465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10109 Z= 0.181 Angle : 0.678 12.576 13662 Z= 0.329 Chirality : 0.042 0.161 1474 Planarity : 0.004 0.059 1749 Dihedral : 5.040 21.532 1350 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.36 % Allowed : 19.92 % Favored : 77.71 % 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: -1.75 (0.24), residues: 1221 helix: 0.12 (0.23), residues: 522 sheet: -1.27 (0.53), residues: 97 loop : -2.38 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 539 HIS 0.003 0.001 HIS B 562 PHE 0.027 0.002 PHE A 504 TYR 0.023 0.001 TYR A 402 ARG 0.008 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 0.2086 time to fit residues: 38.3619 Evaluate side-chains 114 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.276 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.2117 time to fit residues: 6.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 HIS ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10109 Z= 0.238 Angle : 0.701 11.768 13662 Z= 0.347 Chirality : 0.043 0.153 1474 Planarity : 0.004 0.057 1749 Dihedral : 5.225 21.452 1350 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.55 % Allowed : 19.64 % Favored : 77.81 % 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: -1.75 (0.24), residues: 1221 helix: 0.09 (0.23), residues: 524 sheet: -1.47 (0.52), residues: 101 loop : -2.32 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 238 HIS 0.006 0.001 HIS B 562 PHE 0.024 0.002 PHE A 504 TYR 0.021 0.002 TYR A 507 ARG 0.006 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 0.2139 time to fit residues: 37.6894 Evaluate side-chains 113 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.189 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 3 residues processed: 16 average time/residue: 0.1489 time to fit residues: 5.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN ** B 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10109 Z= 0.261 Angle : 0.726 11.744 13662 Z= 0.360 Chirality : 0.044 0.184 1474 Planarity : 0.004 0.057 1749 Dihedral : 5.362 21.772 1350 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.13 % Allowed : 21.06 % Favored : 77.81 % 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: -1.77 (0.24), residues: 1221 helix: 0.02 (0.22), residues: 522 sheet: -1.50 (0.51), residues: 101 loop : -2.27 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 238 HIS 0.005 0.001 HIS B 562 PHE 0.025 0.002 PHE A 504 TYR 0.017 0.002 TYR A 507 ARG 0.005 0.001 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.2324 time to fit residues: 35.6316 Evaluate side-chains 98 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.200 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 739 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.2076 time to fit residues: 3.3009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9923 > 50: distance: 51 - 76: 14.022 distance: 56 - 83: 15.926 distance: 64 - 69: 4.093 distance: 65 - 94: 23.755 distance: 69 - 70: 9.171 distance: 70 - 73: 23.946 distance: 71 - 72: 9.610 distance: 71 - 76: 15.064 distance: 72 - 108: 23.409 distance: 73 - 74: 6.846 distance: 73 - 75: 27.254 distance: 76 - 77: 12.993 distance: 77 - 78: 6.183 distance: 77 - 80: 12.718 distance: 78 - 79: 17.569 distance: 78 - 83: 9.264 distance: 79 - 116: 29.815 distance: 80 - 81: 5.977 distance: 80 - 82: 34.106 distance: 83 - 84: 15.911 distance: 84 - 85: 19.024 distance: 84 - 87: 9.255 distance: 85 - 86: 7.301 distance: 85 - 94: 18.948 distance: 86 - 125: 16.817 distance: 87 - 88: 8.366 distance: 88 - 89: 19.554 distance: 89 - 90: 33.344 distance: 90 - 91: 11.396 distance: 91 - 92: 21.028 distance: 91 - 93: 14.454 distance: 95 - 96: 11.380 distance: 95 - 98: 9.004 distance: 96 - 97: 38.207 distance: 96 - 108: 14.468 distance: 97 - 131: 40.406 distance: 98 - 99: 6.295 distance: 99 - 100: 6.026 distance: 99 - 101: 25.125 distance: 101 - 103: 6.872 distance: 101 - 104: 17.535 distance: 102 - 103: 23.496 distance: 103 - 105: 23.074 distance: 104 - 106: 5.747 distance: 105 - 107: 8.619 distance: 106 - 107: 4.240 distance: 108 - 109: 5.630 distance: 109 - 110: 31.726 distance: 109 - 112: 26.321 distance: 110 - 111: 17.431 distance: 110 - 116: 13.963 distance: 111 - 139: 32.305 distance: 113 - 114: 28.174 distance: 113 - 115: 11.318 distance: 116 - 117: 18.060 distance: 117 - 120: 7.738 distance: 118 - 119: 16.129 distance: 120 - 121: 11.711 distance: 121 - 122: 10.345 distance: 122 - 123: 6.025 distance: 122 - 124: 48.509 distance: 125 - 126: 47.442 distance: 126 - 127: 22.543 distance: 126 - 129: 20.639 distance: 127 - 128: 15.446 distance: 127 - 131: 5.547 distance: 129 - 130: 26.813 distance: 131 - 132: 18.612 distance: 132 - 133: 19.381 distance: 132 - 135: 28.940 distance: 133 - 134: 16.858 distance: 133 - 139: 23.831 distance: 134 - 164: 29.382 distance: 135 - 136: 14.981 distance: 136 - 137: 16.317 distance: 136 - 138: 6.693 distance: 139 - 140: 6.417 distance: 140 - 141: 11.503 distance: 141 - 142: 6.286 distance: 141 - 143: 11.685 distance: 142 - 175: 27.836 distance: 143 - 144: 16.375 distance: 144 - 145: 7.202 distance: 144 - 147: 7.293 distance: 145 - 146: 19.495 distance: 145 - 157: 13.060 distance: 146 - 183: 28.193 distance: 147 - 148: 11.891 distance: 148 - 149: 13.537 distance: 148 - 150: 6.115 distance: 149 - 151: 3.112 distance: 150 - 152: 6.212 distance: 152 - 154: 5.538 distance: 153 - 155: 3.043 distance: 154 - 156: 3.717 distance: 155 - 156: 4.664