Starting phenix.real_space_refine (version: dev) on Tue Mar 14 03:15:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2023/7r8b_24314_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.059 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 Process input model Symmetric amino acids flipped Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 10868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 3 Chain: "B" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4482 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 3 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.50, per 1000 atoms: 0.60 Number of scatterers: 10868 At special positions: 0 Unit cell: (114.121, 105.791, 122.451, 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 67 16.00 O 1936 8.00 N 1838 7.00 C 7027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 8 sheets defined 47.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 195 through 209 removed outlier: 4.573A pdb=" N GLN A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 331 Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 364 through 380 Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.299A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 453 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 460 through 490 Proline residue: A 473 - end of helix removed outlier: 4.877A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 523 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 527 through 544 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.771A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 606 through 612 Processing helix chain 'A' and resid 614 through 647 removed outlier: 4.428A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 620 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR A 621 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 630 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 631 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 3.604A pdb=" N ASP A 646 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 245 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.600A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.560A pdb=" N ALA B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 335 through 352 removed outlier: 4.051A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 4.041A pdb=" N ARG B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 445 through 457 Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 491 through 516 Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'B' and resid 595 through 607 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 640 through 664 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing sheet with id= A, first strand: chain 'A' and resid 74 through 77 removed outlier: 4.773A pdb=" N VAL A 113 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.581A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 245 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= D, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.731A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 265 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 103 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE B 267 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY B 105 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= F, first strand: chain 'C' and resid 116 through 118 removed outlier: 5.865A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 24 through 27 Processing sheet with id= H, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.013A pdb=" N LYS D 123 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS D 59 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE D 64 " --> pdb=" O LYS D 59 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3453 1.34 - 1.46: 2633 1.46 - 1.58: 4913 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 11106 Sorted by residual: bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.49e+00 bond pdb=" CA LYS B 126 " pdb=" CB LYS B 126 " ideal model delta sigma weight residual 1.526 1.545 -0.020 1.68e-02 3.54e+03 1.37e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.25e+00 bond pdb=" C3 CLR A 701 " pdb=" O1 CLR A 701 " ideal model delta sigma weight residual 1.413 1.391 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA THR A 430 " pdb=" C THR A 430 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.08e+00 ... (remaining 11101 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 305 107.01 - 113.75: 6069 113.75 - 120.49: 4474 120.49 - 127.23: 4094 127.23 - 133.97: 99 Bond angle restraints: 15041 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C VAL A 404 " pdb=" N LEU A 405 " pdb=" CA LEU A 405 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ALA D 70 " pdb=" N ALA D 71 " pdb=" CA ALA D 71 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 111.91 109.05 2.86 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 111.90 109.40 2.50 8.10e-01 1.52e+00 9.53e+00 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5984 17.40 - 34.81: 493 34.81 - 52.21: 91 52.21 - 69.61: 25 69.61 - 87.02: 7 Dihedral angle restraints: 6600 sinusoidal: 2642 harmonic: 3958 Sorted by residual: dihedral pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " ideal model delta sinusoidal sigma weight residual 60.00 119.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A 122 " pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -118.56 58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET B 558 " pdb=" CG MET B 558 " pdb=" SD MET B 558 " pdb=" CE MET B 558 " ideal model delta sinusoidal sigma weight residual -60.00 -2.80 -57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1597 0.072 - 0.143: 112 0.143 - 0.215: 2 0.215 - 0.286: 3 0.286 - 0.358: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C14 CLR B 801 " pdb=" C13 CLR B 801 " pdb=" C15 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C14 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C15 CLR A 701 " pdb=" C8 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C9 CLR B 801 " pdb=" C10 CLR B 801 " pdb=" C11 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.69 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1713 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 126 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C LYS B 126 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS B 126 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE B 127 " -0.007 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 157 2.66 - 3.22: 9906 3.22 - 3.78: 16859 3.78 - 4.34: 23085 4.34 - 4.90: 38684 Nonbonded interactions: 88691 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" OG1 THR D 42 " model vdw 2.103 2.440 nonbonded pdb=" O VAL A 542 " pdb=" OG SER A 546 " model vdw 2.204 2.440 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.258 2.440 nonbonded pdb=" O ASN A 410 " pdb=" OG1 THR A 586 " model vdw 2.267 2.440 nonbonded pdb=" NE ARG A 550 " pdb=" O LEU B 434 " model vdw 2.290 2.520 ... (remaining 88686 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7027 2.51 5 N 1838 2.21 5 O 1936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 6.200 Check model and map are aligned: 0.170 Process input model: 31.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.002 0.032 11106 Z= 0.131 Angle : 0.553 7.058 15041 Z= 0.314 Chirality : 0.040 0.358 1716 Planarity : 0.003 0.035 1884 Dihedral : 13.480 87.019 4051 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.73 (0.21), residues: 1351 helix: 0.06 (0.18), residues: 702 sheet: -1.48 (0.35), residues: 182 loop : -2.85 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.200 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.2849 time to fit residues: 87.9086 Evaluate side-chains 152 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1060 time to fit residues: 3.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 160 ASN A 165 GLN A 179 HIS A 206 GLN A 230 GLN A 347 HIS A 378 ASN A 437 ASN A 454 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 578 ASN A 597 ASN A 604 GLN A 607 GLN B 43 GLN B 99 GLN B 153 GLN B 172 GLN B 250 ASN B 262 ASN B 271 GLN B 438 HIS B 526 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 75 ASN D 57 GLN D 58 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11106 Z= 0.200 Angle : 0.532 10.002 15041 Z= 0.264 Chirality : 0.040 0.233 1716 Planarity : 0.004 0.034 1884 Dihedral : 3.712 52.922 1520 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.51 (0.23), residues: 1351 helix: 1.10 (0.20), residues: 703 sheet: -0.96 (0.37), residues: 187 loop : -2.36 (0.27), residues: 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.218 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 172 average time/residue: 0.2496 time to fit residues: 60.3986 Evaluate side-chains 159 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1048 time to fit residues: 5.5862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 98 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS B 172 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 11106 Z= 0.156 Angle : 0.491 7.944 15041 Z= 0.244 Chirality : 0.039 0.175 1716 Planarity : 0.003 0.034 1884 Dihedral : 3.726 54.645 1520 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.23), residues: 1351 helix: 1.45 (0.20), residues: 702 sheet: -0.76 (0.36), residues: 193 loop : -2.04 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.387 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 159 average time/residue: 0.2671 time to fit residues: 59.5375 Evaluate side-chains 147 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1030 time to fit residues: 4.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 0.0010 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 160 ASN A 165 GLN A 470 HIS A 531 ASN B 135 ASN B 172 GLN B 199 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.052 11106 Z= 0.476 Angle : 0.649 9.674 15041 Z= 0.326 Chirality : 0.046 0.197 1716 Planarity : 0.004 0.034 1884 Dihedral : 4.354 50.444 1520 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.22 (0.23), residues: 1351 helix: 1.12 (0.20), residues: 696 sheet: -0.51 (0.37), residues: 188 loop : -1.93 (0.28), residues: 467 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.253 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 148 average time/residue: 0.2638 time to fit residues: 54.4069 Evaluate side-chains 139 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1025 time to fit residues: 4.8468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 111 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 11106 Z= 0.142 Angle : 0.516 11.913 15041 Z= 0.258 Chirality : 0.039 0.163 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.029 54.893 1520 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1351 helix: 1.53 (0.20), residues: 694 sheet: -0.34 (0.37), residues: 188 loop : -1.72 (0.29), residues: 469 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.352 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 0.2862 time to fit residues: 57.0073 Evaluate side-chains 135 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1135 time to fit residues: 4.0756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 11106 Z= 0.295 Angle : 0.581 12.798 15041 Z= 0.287 Chirality : 0.042 0.205 1716 Planarity : 0.004 0.031 1884 Dihedral : 4.153 54.306 1520 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1351 helix: 1.48 (0.20), residues: 696 sheet: -0.27 (0.37), residues: 188 loop : -1.66 (0.29), residues: 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.313 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.2877 time to fit residues: 50.3181 Evaluate side-chains 128 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1165 time to fit residues: 3.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11106 Z= 0.219 Angle : 0.555 12.722 15041 Z= 0.273 Chirality : 0.041 0.188 1716 Planarity : 0.003 0.031 1884 Dihedral : 4.109 56.276 1520 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.40 (0.24), residues: 1351 helix: 1.57 (0.20), residues: 696 sheet: -0.16 (0.38), residues: 188 loop : -1.58 (0.29), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.272 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 128 average time/residue: 0.2857 time to fit residues: 50.2090 Evaluate side-chains 122 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1120 time to fit residues: 2.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11106 Z= 0.198 Angle : 0.558 13.495 15041 Z= 0.272 Chirality : 0.040 0.176 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.088 58.181 1520 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.51 (0.24), residues: 1351 helix: 1.67 (0.20), residues: 697 sheet: -0.13 (0.37), residues: 188 loop : -1.53 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.432 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.3426 time to fit residues: 57.4290 Evaluate side-chains 118 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2657 time to fit residues: 3.8264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11106 Z= 0.223 Angle : 0.562 13.835 15041 Z= 0.276 Chirality : 0.041 0.204 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.132 59.829 1520 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.55 (0.24), residues: 1351 helix: 1.69 (0.20), residues: 696 sheet: -0.11 (0.37), residues: 188 loop : -1.49 (0.29), residues: 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.341 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 116 average time/residue: 0.3075 time to fit residues: 48.3764 Evaluate side-chains 115 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1370 time to fit residues: 2.2326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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: 63.4501 > 50: distance: 9 - 15: 6.724 distance: 15 - 16: 24.109 distance: 15 - 21: 13.167 distance: 16 - 17: 27.354 distance: 16 - 19: 15.185 distance: 17 - 18: 3.451 distance: 17 - 22: 26.728 distance: 19 - 20: 26.159 distance: 20 - 21: 14.138 distance: 22 - 23: 17.878 distance: 23 - 24: 23.988 distance: 23 - 26: 16.084 distance: 24 - 25: 19.968 distance: 24 - 30: 11.563 distance: 26 - 27: 19.646 distance: 27 - 28: 6.846 distance: 27 - 29: 19.846 distance: 30 - 31: 13.670 distance: 31 - 32: 24.143 distance: 31 - 34: 19.393 distance: 32 - 33: 15.812 distance: 32 - 37: 10.342 distance: 34 - 35: 39.104 distance: 34 - 36: 27.806 distance: 37 - 38: 10.657 distance: 37 - 155: 26.521 distance: 38 - 39: 10.280 distance: 38 - 41: 12.830 distance: 39 - 40: 21.732 distance: 39 - 45: 20.405 distance: 40 - 152: 24.709 distance: 41 - 42: 28.574 distance: 42 - 43: 20.304 distance: 42 - 44: 15.425 distance: 45 - 46: 16.831 distance: 45 - 215: 19.269 distance: 46 - 49: 12.819 distance: 47 - 48: 8.826 distance: 48 - 212: 16.697 distance: 49 - 50: 9.225 distance: 50 - 51: 16.595 distance: 51 - 52: 6.944 distance: 51 - 53: 5.586 distance: 54 - 55: 5.480 distance: 54 - 136: 13.800 distance: 55 - 56: 3.983 distance: 55 - 58: 7.986 distance: 56 - 57: 5.028 distance: 56 - 61: 9.396 distance: 57 - 133: 16.623 distance: 58 - 60: 4.162 distance: 61 - 62: 5.864 distance: 61 - 200: 21.747 distance: 62 - 63: 7.845 distance: 62 - 65: 14.774 distance: 63 - 64: 13.850 distance: 63 - 72: 14.314 distance: 64 - 197: 21.328 distance: 65 - 66: 9.049 distance: 66 - 67: 10.956 distance: 67 - 68: 6.316 distance: 68 - 69: 13.344 distance: 69 - 70: 13.855 distance: 69 - 71: 15.958 distance: 72 - 73: 9.448 distance: 73 - 74: 4.922 distance: 73 - 76: 7.503 distance: 74 - 80: 13.669 distance: 76 - 77: 11.673 distance: 77 - 78: 4.714 distance: 77 - 79: 5.375 distance: 80 - 81: 55.462 distance: 81 - 82: 29.116 distance: 81 - 84: 19.983 distance: 82 - 83: 17.057 distance: 82 - 88: 24.914 distance: 84 - 85: 9.354 distance: 85 - 87: 17.741 distance: 88 - 89: 8.834 distance: 89 - 90: 20.463 distance: 89 - 92: 28.502 distance: 90 - 91: 26.640 distance: 90 - 96: 28.871 distance: 92 - 93: 14.763 distance: 93 - 95: 41.118