Starting phenix.real_space_refine on Sat Jul 20 12:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3c_36849/07_2024/8k3c_36849.cif" } resolution = 2.88 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 6844 2.51 5 N 1824 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10813 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1778 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 224} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3710 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 437} Chain: "B" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3718 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 438} Time building chain proxies: 8.42, per 1000 atoms: 0.78 Number of scatterers: 10813 At special positions: 0 Unit cell: (95.12, 109.88, 176.3, 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 61 16.00 O 2084 8.00 N 1824 7.00 C 6844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 197 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.02 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.01 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.02 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.02 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: 3.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 27 sheets defined 7.5% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 125 through 131 removed outlier: 4.222A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.352A pdb=" N SER C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N CYS B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 121 removed outlier: 3.696A pdb=" N LEU D 182 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D 142 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR D 176 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.888A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR C 125 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.765A pdb=" N CYS C 214 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 227 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 216 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.744A pdb=" N LYS A 199 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A 596 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 216 through 224 removed outlier: 6.282A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.286A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB7, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.800A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.590A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 557 through 567 removed outlier: 3.922A pdb=" N ASN A 557 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU A 579 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR A 561 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 577 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR A 563 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 575 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 565 " --> pdb=" O TRP A 573 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP A 573 " --> pdb=" O CYS A 565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 178 through 179 removed outlier: 5.965A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 587 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.557A pdb=" N PHE B 229 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.398A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.808A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC8, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.512A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 465 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 511 through 513 removed outlier: 4.971A pdb=" N GLN B 550 " --> pdb=" O PRO B 535 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B 537 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 999 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: 4.03 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3412 1.34 - 1.46: 2844 1.46 - 1.59: 4744 1.59 - 1.72: 0 1.72 - 1.84: 78 Bond restraints: 11078 Sorted by residual: bond pdb=" C SER A 390 " pdb=" N LYS A 391 " ideal model delta sigma weight residual 1.329 1.237 0.091 1.60e-02 3.91e+03 3.25e+01 bond pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N ILE D 140 " pdb=" CA ILE D 140 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N VAL D 119 " pdb=" CA VAL D 119 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" CB ILE A 356 " pdb=" CG2 ILE A 356 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.06e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 93.21 - 101.71: 20 101.71 - 110.22: 3043 110.22 - 118.72: 5918 118.72 - 127.23: 5955 127.23 - 135.73: 155 Bond angle restraints: 15091 Sorted by residual: angle pdb=" N PRO D 123 " pdb=" CA PRO D 123 " pdb=" C PRO D 123 " ideal model delta sigma weight residual 110.70 117.59 -6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 123.60 -9.70 1.80e+00 3.09e-01 2.91e+01 angle pdb=" C THR B 218 " pdb=" N ASP B 219 " pdb=" CA ASP B 219 " ideal model delta sigma weight residual 122.83 128.51 -5.68 1.08e+00 8.57e-01 2.76e+01 angle pdb=" CB MET B 267 " pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 112.70 97.15 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C THR C 237 " pdb=" N SER C 238 " pdb=" CA SER C 238 " ideal model delta sigma weight residual 121.70 130.89 -9.19 1.80e+00 3.09e-01 2.61e+01 ... (remaining 15086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6390 17.73 - 35.46: 244 35.46 - 53.19: 62 53.19 - 70.92: 5 70.92 - 88.65: 4 Dihedral angle restraints: 6705 sinusoidal: 2653 harmonic: 4052 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -174.65 88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CA GLY C 53 " pdb=" C GLY C 53 " pdb=" N SER C 54 " pdb=" CA SER C 54 " ideal model delta harmonic sigma weight residual -180.00 -140.63 -39.37 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1279 0.075 - 0.149: 356 0.149 - 0.224: 37 0.224 - 0.298: 8 0.298 - 0.373: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CB ILE B 444 " pdb=" CA ILE B 444 " pdb=" CG1 ILE B 444 " pdb=" CG2 ILE B 444 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB ILE A 444 " pdb=" CA ILE A 444 " pdb=" CG1 ILE A 444 " pdb=" CG2 ILE A 444 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1679 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 292 " -0.029 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 292 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 292 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 292 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 292 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 292 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 292 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 168 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C PHE B 168 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE B 168 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 169 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " -0.019 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " -0.000 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 476 2.69 - 3.24: 10072 3.24 - 3.80: 18651 3.80 - 4.35: 23532 4.35 - 4.90: 39709 Nonbonded interactions: 92440 Sorted by model distance: nonbonded pdb=" CB ALA D 115 " pdb=" N TYR D 144 " model vdw 2.138 3.540 nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.197 2.440 nonbonded pdb=" OG SER A 528 " pdb=" O THR A 531 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 205 " pdb=" OH TYR A 231 " model vdw 2.224 2.440 nonbonded pdb=" OG SER B 298 " pdb=" O GLY B 301 " model vdw 2.261 2.440 ... (remaining 92435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 132 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 14.490 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 36.230 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.014 0.118 11078 Z= 0.947 Angle : 1.171 15.554 15091 Z= 0.659 Chirality : 0.067 0.373 1682 Planarity : 0.008 0.068 1953 Dihedral : 10.350 79.053 4057 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 0.57 % Allowed : 2.44 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.15 % 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: -3.08 (0.20), residues: 1387 helix: -1.99 (0.50), residues: 66 sheet: -1.94 (0.22), residues: 476 loop : -2.15 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP B 519 HIS 0.013 0.002 HIS A 233 PHE 0.057 0.006 PHE B 364 TYR 0.060 0.005 TYR B 292 ARG 0.014 0.002 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ARG cc_start: 0.4668 (mtm-85) cc_final: 0.3794 (mtt-85) REVERT: D 97 HIS cc_start: 0.6829 (m90) cc_final: 0.6440 (m-70) REVERT: D 212 PRO cc_start: 0.4885 (Cg_endo) cc_final: 0.4684 (Cg_exo) REVERT: C 34 MET cc_start: 0.6443 (mmm) cc_final: 0.5865 (mmm) REVERT: C 39 GLN cc_start: 0.5983 (tt0) cc_final: 0.5643 (tt0) REVERT: C 93 VAL cc_start: 0.6082 (t) cc_final: 0.5814 (p) REVERT: C 197 SER cc_start: 0.6115 (m) cc_final: 0.5707 (t) REVERT: A 381 ASN cc_start: 0.8349 (m-40) cc_final: 0.7991 (m-40) REVERT: A 391 LYS cc_start: 0.7348 (mtmt) cc_final: 0.6985 (ptpp) REVERT: A 425 LYS cc_start: 0.7135 (pttt) cc_final: 0.6869 (ptpp) REVERT: A 437 SER cc_start: 0.7316 (p) cc_final: 0.6947 (m) REVERT: A 501 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5945 (mm-30) REVERT: A 554 GLU cc_start: 0.6248 (tt0) cc_final: 0.5647 (tm-30) REVERT: A 589 ARG cc_start: 0.5795 (mtm180) cc_final: 0.4935 (mtp85) REVERT: B 199 LYS cc_start: 0.8082 (mttt) cc_final: 0.7678 (mmtp) REVERT: B 254 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6777 (mp0) REVERT: B 374 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 388 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6607 (tm-30) REVERT: B 389 TYR cc_start: 0.7984 (m-10) cc_final: 0.7295 (m-80) REVERT: B 399 MET cc_start: 0.7924 (mmm) cc_final: 0.7581 (mmm) REVERT: B 519 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6391 (t60) REVERT: B 527 ASP cc_start: 0.6327 (t70) cc_final: 0.6066 (t0) REVERT: B 550 GLN cc_start: 0.6973 (pt0) cc_final: 0.6334 (tt0) REVERT: B 569 LYS cc_start: 0.6103 (mtmm) cc_final: 0.5503 (mptt) REVERT: B 588 ILE cc_start: 0.7546 (mt) cc_final: 0.7099 (tp) REVERT: B 599 GLU cc_start: 0.6789 (mp0) cc_final: 0.6512 (tt0) outliers start: 7 outliers final: 5 residues processed: 214 average time/residue: 1.1378 time to fit residues: 265.8096 Evaluate side-chains 126 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.0040 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN D 39 GLN D 171 GLN C 123 GLN C 189 GLN A 139 ASN A 159 ASN A 164 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 269 ASN A 287 ASN A 306 ASN A 333 HIS A 406 HIS A 423 ASN A 434 GLN A 529 ASN A 557 ASN B 141 ASN B 156 HIS B 195 ASN B 277 ASN B 406 HIS B 455 GLN B 478 ASN B 530 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11078 Z= 0.212 Angle : 0.633 8.936 15091 Z= 0.333 Chirality : 0.047 0.200 1682 Planarity : 0.005 0.046 1953 Dihedral : 6.592 56.759 1521 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.54 % Allowed : 8.53 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.38 (0.21), residues: 1387 helix: -1.05 (0.56), residues: 67 sheet: -1.52 (0.22), residues: 477 loop : -1.67 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 519 HIS 0.005 0.001 HIS B 233 PHE 0.024 0.002 PHE B 229 TYR 0.027 0.002 TYR A 351 ARG 0.006 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.6880 (m-80) cc_final: 0.6328 (m-80) REVERT: D 55 ARG cc_start: 0.4568 (mtm-85) cc_final: 0.3980 (mtt90) REVERT: D 70 THR cc_start: 0.7762 (p) cc_final: 0.7311 (t) REVERT: D 97 HIS cc_start: 0.6418 (m90) cc_final: 0.6045 (m-70) REVERT: C 30 SER cc_start: 0.5471 (p) cc_final: 0.4910 (t) REVERT: C 34 MET cc_start: 0.6455 (mmm) cc_final: 0.6054 (mmm) REVERT: C 39 GLN cc_start: 0.5925 (tt0) cc_final: 0.5720 (tt0) REVERT: C 177 LEU cc_start: 0.3384 (tm) cc_final: 0.2803 (mm) REVERT: A 315 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.6011 (pmt) REVERT: A 378 ASN cc_start: 0.6798 (t0) cc_final: 0.6493 (t0) REVERT: A 381 ASN cc_start: 0.8225 (m-40) cc_final: 0.7844 (m-40) REVERT: A 391 LYS cc_start: 0.7281 (mtmt) cc_final: 0.6907 (pttm) REVERT: A 402 ARG cc_start: 0.7093 (ptt-90) cc_final: 0.6428 (mtm110) REVERT: A 425 LYS cc_start: 0.7095 (pttt) cc_final: 0.6671 (ptpp) REVERT: A 437 SER cc_start: 0.7435 (p) cc_final: 0.6794 (m) REVERT: A 501 GLU cc_start: 0.6063 (mm-30) cc_final: 0.5784 (mm-30) REVERT: A 554 GLU cc_start: 0.6236 (tt0) cc_final: 0.5676 (tm-30) REVERT: A 589 ARG cc_start: 0.5813 (mtm180) cc_final: 0.4995 (mtp85) REVERT: B 191 GLN cc_start: 0.7802 (mp10) cc_final: 0.6952 (mm-40) REVERT: B 199 LYS cc_start: 0.8039 (mttt) cc_final: 0.7646 (mmtp) REVERT: B 254 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6764 (mp0) REVERT: B 374 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 388 GLN cc_start: 0.6989 (mm-40) cc_final: 0.6555 (tm-30) REVERT: B 399 MET cc_start: 0.7751 (mmm) cc_final: 0.7347 (mmm) REVERT: B 519 TRP cc_start: 0.7125 (OUTLIER) cc_final: 0.4618 (t60) REVERT: B 527 ASP cc_start: 0.6256 (t70) cc_final: 0.5756 (t0) REVERT: B 550 GLN cc_start: 0.6767 (pt0) cc_final: 0.6034 (tt0) REVERT: B 569 LYS cc_start: 0.6081 (mtmm) cc_final: 0.5487 (mptt) REVERT: B 588 ILE cc_start: 0.7512 (mt) cc_final: 0.7138 (tp) REVERT: B 599 GLU cc_start: 0.6882 (mp0) cc_final: 0.6478 (tt0) outliers start: 19 outliers final: 10 residues processed: 172 average time/residue: 0.9276 time to fit residues: 175.9096 Evaluate side-chains 136 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 585 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN D 192 HIS C 77 ASN C 82 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 388 GLN A 417 ASN A 455 GLN B 156 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11078 Z= 0.345 Angle : 0.660 8.222 15091 Z= 0.345 Chirality : 0.049 0.264 1682 Planarity : 0.006 0.049 1953 Dihedral : 6.335 70.735 1516 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.25 % Allowed : 9.99 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.10 (0.22), residues: 1387 helix: 0.32 (0.68), residues: 61 sheet: -1.24 (0.23), residues: 479 loop : -1.64 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.005 0.001 HIS D 33 PHE 0.042 0.003 PHE D 143 TYR 0.034 0.002 TYR C 114 ARG 0.005 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7306 (m-80) cc_final: 0.6537 (m-80) REVERT: D 55 ARG cc_start: 0.4579 (mtm-85) cc_final: 0.3859 (mtt90) REVERT: D 97 HIS cc_start: 0.6090 (m90) cc_final: 0.5464 (m90) REVERT: D 139 LEU cc_start: 0.5392 (mm) cc_final: 0.5092 (mm) REVERT: C 177 LEU cc_start: 0.3391 (OUTLIER) cc_final: 0.2802 (mm) REVERT: A 242 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6675 (mtm180) REVERT: A 261 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: A 346 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.5806 (t0) REVERT: A 378 ASN cc_start: 0.7140 (t0) cc_final: 0.6895 (t0) REVERT: A 382 CYS cc_start: 0.5788 (t) cc_final: 0.5462 (t) REVERT: A 402 ARG cc_start: 0.7094 (ptt-90) cc_final: 0.6269 (mtm110) REVERT: A 420 ASP cc_start: 0.5684 (m-30) cc_final: 0.5363 (m-30) REVERT: A 425 LYS cc_start: 0.7114 (pttt) cc_final: 0.6705 (ptpp) REVERT: A 554 GLU cc_start: 0.6113 (tt0) cc_final: 0.5526 (tm-30) REVERT: A 569 LYS cc_start: 0.7149 (mttm) cc_final: 0.6916 (mttt) REVERT: A 589 ARG cc_start: 0.6021 (mtm180) cc_final: 0.5049 (mtt90) REVERT: B 191 GLN cc_start: 0.7831 (mt0) cc_final: 0.7019 (mm-40) REVERT: B 199 LYS cc_start: 0.8072 (mttt) cc_final: 0.7711 (mmtp) REVERT: B 217 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5693 (mm) REVERT: B 254 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6747 (mt-10) REVERT: B 519 TRP cc_start: 0.7516 (OUTLIER) cc_final: 0.5597 (t60) REVERT: B 527 ASP cc_start: 0.6344 (t70) cc_final: 0.5811 (t0) REVERT: B 550 GLN cc_start: 0.6761 (pt0) cc_final: 0.6406 (mt0) REVERT: B 559 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: B 569 LYS cc_start: 0.6066 (mtmm) cc_final: 0.5524 (mptt) REVERT: B 588 ILE cc_start: 0.7395 (mt) cc_final: 0.7019 (tp) REVERT: B 599 GLU cc_start: 0.6969 (mp0) cc_final: 0.6528 (tt0) outliers start: 40 outliers final: 20 residues processed: 158 average time/residue: 0.9724 time to fit residues: 169.8469 Evaluate side-chains 143 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 559 GLN Chi-restraints excluded: chain B residue 571 LYS Chi-restraints excluded: chain B residue 585 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.1980 chunk 94 optimal weight: 0.0770 chunk 65 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN C 189 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN B 333 HIS B 509 ASN B 586 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11078 Z= 0.196 Angle : 0.575 7.870 15091 Z= 0.297 Chirality : 0.046 0.187 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.801 71.762 1516 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.92 % Allowed : 11.13 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.86 (0.22), residues: 1387 helix: 0.98 (0.73), residues: 61 sheet: -1.10 (0.22), residues: 490 loop : -1.50 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.008 0.001 HIS B 233 PHE 0.032 0.002 PHE B 229 TYR 0.031 0.002 TYR C 114 ARG 0.005 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7269 (m-80) cc_final: 0.6579 (m-80) REVERT: D 55 ARG cc_start: 0.4335 (mtm-85) cc_final: 0.3461 (mtt90) REVERT: D 97 HIS cc_start: 0.5787 (m90) cc_final: 0.5212 (m90) REVERT: D 139 LEU cc_start: 0.5170 (mm) cc_final: 0.4859 (mm) REVERT: C 49 SER cc_start: 0.7194 (p) cc_final: 0.6820 (t) REVERT: C 60 TYR cc_start: 0.6572 (m-80) cc_final: 0.5343 (m-80) REVERT: C 177 LEU cc_start: 0.3394 (OUTLIER) cc_final: 0.2803 (mm) REVERT: A 195 ASN cc_start: 0.6285 (m110) cc_final: 0.6082 (m-40) REVERT: A 236 ARG cc_start: 0.5583 (mtt180) cc_final: 0.5245 (ttm170) REVERT: A 242 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6670 (mtm180) REVERT: A 381 ASN cc_start: 0.8152 (m-40) cc_final: 0.7913 (m-40) REVERT: A 402 ARG cc_start: 0.7132 (ptt-90) cc_final: 0.6276 (mtm110) REVERT: A 420 ASP cc_start: 0.5674 (m-30) cc_final: 0.5387 (m-30) REVERT: A 425 LYS cc_start: 0.6958 (pttt) cc_final: 0.6586 (ptpp) REVERT: A 554 GLU cc_start: 0.6068 (tt0) cc_final: 0.5503 (tm-30) REVERT: A 589 ARG cc_start: 0.5820 (mtm180) cc_final: 0.5007 (mtt90) REVERT: B 191 GLN cc_start: 0.7791 (mt0) cc_final: 0.7017 (mm-40) REVERT: B 199 LYS cc_start: 0.8029 (mttt) cc_final: 0.7705 (mmtp) REVERT: B 217 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5509 (mm) REVERT: B 254 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6755 (mp0) REVERT: B 388 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 519 TRP cc_start: 0.7311 (OUTLIER) cc_final: 0.4639 (t60) REVERT: B 527 ASP cc_start: 0.6340 (t70) cc_final: 0.5874 (t0) REVERT: B 550 GLN cc_start: 0.6588 (pt0) cc_final: 0.6300 (mt0) REVERT: B 559 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6670 (tp-100) REVERT: B 569 LYS cc_start: 0.5959 (mtmm) cc_final: 0.5453 (mptt) REVERT: B 588 ILE cc_start: 0.7362 (mt) cc_final: 0.6940 (tp) REVERT: B 599 GLU cc_start: 0.7037 (mp0) cc_final: 0.6562 (tt0) outliers start: 36 outliers final: 14 residues processed: 152 average time/residue: 0.9484 time to fit residues: 159.6690 Evaluate side-chains 133 residues out of total 1231 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 559 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9376 > 50: distance: 82 - 86: 35.943 distance: 86 - 87: 56.582 distance: 86 - 92: 44.575 distance: 87 - 88: 40.423 distance: 88 - 89: 39.056 distance: 90 - 91: 39.910 distance: 91 - 92: 21.592 distance: 94 - 97: 40.282 distance: 95 - 99: 39.260 distance: 97 - 98: 40.632 distance: 99 - 100: 48.982 distance: 99 - 191: 32.099 distance: 100 - 101: 12.977 distance: 100 - 103: 28.448 distance: 101 - 102: 40.943 distance: 101 - 108: 48.634 distance: 102 - 188: 34.210 distance: 103 - 104: 57.642 distance: 105 - 106: 55.442 distance: 108 - 109: 27.169 distance: 109 - 110: 39.214 distance: 109 - 112: 36.737 distance: 110 - 111: 38.689 distance: 112 - 113: 53.969 distance: 112 - 114: 57.065 distance: 113 - 115: 40.799 distance: 116 - 117: 41.166 distance: 116 - 173: 32.070 distance: 117 - 118: 40.245 distance: 117 - 120: 25.669 distance: 118 - 119: 40.357 distance: 118 - 128: 40.647 distance: 119 - 170: 33.610 distance: 120 - 121: 28.226 distance: 121 - 123: 24.092 distance: 122 - 124: 40.029 distance: 123 - 125: 33.695 distance: 124 - 126: 21.150 distance: 125 - 126: 18.887 distance: 126 - 127: 40.216 distance: 128 - 129: 19.411 distance: 129 - 130: 19.146 distance: 129 - 132: 26.078 distance: 130 - 131: 39.199 distance: 132 - 133: 44.907 distance: 133 - 135: 56.183 distance: 136 - 137: 47.513 distance: 137 - 138: 38.796 distance: 137 - 140: 46.218 distance: 138 - 142: 38.885 distance: 140 - 141: 67.714 distance: 142 - 143: 47.403 distance: 143 - 144: 31.195 distance: 143 - 146: 14.936 distance: 144 - 145: 25.700 distance: 144 - 150: 13.894 distance: 147 - 148: 55.596 distance: 151 - 152: 41.023 distance: 152 - 153: 44.079 distance: 155 - 158: 39.805 distance: 156 - 157: 21.742 distance: 156 - 163: 35.194 distance: 159 - 160: 57.005 distance: 160 - 161: 40.946