Starting phenix.real_space_refine (version: dev) on Tue Apr 5 13:12:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugh_20764/04_2022/6ugh_20764.pdb" } resolution = 3.4 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= 0.000 sd= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 189": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 13690 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9309 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 594, 9309 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 553, 'PCIS': 4} Chain breaks: 4 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4381 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 11, 'TRANS': 288, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 187 " occ=0.50 ... (15 atoms not shown) pdb=" HE3AMET A 187 " occ=0.50 Time building chain proxies: 6.90, per 1000 atoms: 0.50 Number of scatterers: 13690 At special positions: 0 Unit cell: (85.8, 71.28, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 1301 8.00 N 1200 7.00 C 4438 6.00 H 6716 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 26.1% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.527A pdb=" N ASN A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.571A pdb=" N LEU A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 96 through 118 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.535A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.567A pdb=" N ARG A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.516A pdb=" N AMET A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.010A pdb=" N ARG A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.127A pdb=" N LEU A 253 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.307A pdb=" N GLU A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 277 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.899A pdb=" N LEU A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 330 through 349 removed outlier: 3.688A pdb=" N TYR A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.750A pdb=" N LYS A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 removed outlier: 3.819A pdb=" N ALA A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 removed outlier: 4.439A pdb=" N THR A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.549A pdb=" N ASN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.585A pdb=" N HIS A 572 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.556A pdb=" N GLY A 630 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 631 " --> pdb=" O PRO A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 627 through 631' Processing helix chain 'B' and resid 69 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.980A pdb=" N SER A 16 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS A 42 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 18 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 41 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS A 85 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU A 123 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 84 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 122 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 154 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 124 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE A 151 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 205 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N MET A 153 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU A 207 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 155 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE A 226 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 204 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY A 17 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 416 removed outlier: 8.295A pdb=" N THR A 414 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 388 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 416 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A 390 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 360 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 433 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET A 362 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA A 429 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP A 460 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 431 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 462 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 433 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 464 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 503 removed outlier: 3.906A pdb=" N ILE A 586 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N HIS A 549 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N GLN A 588 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL A 547 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR A 468 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A 520 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A 470 " --> pdb=" O CYS A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511 removed outlier: 7.212A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 541 removed outlier: 6.466A pdb=" N CYS A 599 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 36 removed outlier: 3.525A pdb=" N GLN B 30 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 45 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA B 34 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 43 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 89 removed outlier: 3.528A pdb=" N GLY B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 103 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N CYS B 120 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 105 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.673A pdb=" N THR B 130 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 149 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER B 162 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 151 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.683A pdb=" N CYS B 172 " --> pdb=" O CYS B 186 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 192 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 220 removed outlier: 6.550A pdb=" N GLY B 231 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 218 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 229 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP B 220 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL B 227 " --> pdb=" O TRP B 220 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 249 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.781A pdb=" N PHE B 291 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 300 through 305 removed outlier: 7.057A pdb=" N VAL B 316 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 303 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 314 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP B 305 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 312 " --> pdb=" O TRP B 305 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 669 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: 5.29 Time building geometry restraints manager: 11.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6692 1.03 - 1.23: 84 1.23 - 1.42: 3007 1.42 - 1.62: 4039 1.62 - 1.81: 46 Bond restraints: 13868 Sorted by residual: bond pdb=" CG PRO A 465 " pdb=" CD PRO A 465 " ideal model delta sigma weight residual 1.512 1.453 0.059 2.70e-02 1.37e+03 4.74e+00 bond pdb=" CB TRP A 189 " pdb=" CG TRP A 189 " ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.26e+00 bond pdb=" CB PRO A 465 " pdb=" CG PRO A 465 " ideal model delta sigma weight residual 1.506 1.426 0.080 3.90e-02 6.57e+02 4.24e+00 bond pdb=" CA ASN A 627 " pdb=" C ASN A 627 " ideal model delta sigma weight residual 1.532 1.519 0.013 6.50e-03 2.37e+04 4.02e+00 bond pdb=" CB PRO A 501 " pdb=" CG PRO A 501 " ideal model delta sigma weight residual 1.492 1.392 0.100 5.00e-02 4.00e+02 4.02e+00 ... (remaining 13863 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.57: 274 105.57 - 112.73: 15554 112.73 - 119.89: 3868 119.89 - 127.05: 5178 127.05 - 134.21: 140 Bond angle restraints: 25014 Sorted by residual: angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" C VAL B 248 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" C GLU A 276 " pdb=" N PHE A 277 " pdb=" CA PHE A 277 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.40e+01 angle pdb=" N TYR A 560 " pdb=" CA TYR A 560 " pdb=" C TYR A 560 " ideal model delta sigma weight residual 108.38 103.38 5.00 1.35e+00 5.49e-01 1.37e+01 angle pdb=" N GLY A 369 " pdb=" CA GLY A 369 " pdb=" C GLY A 369 " ideal model delta sigma weight residual 112.34 119.38 -7.04 2.04e+00 2.40e-01 1.19e+01 angle pdb=" N VAL A 504 " pdb=" CA VAL A 504 " pdb=" C VAL A 504 " ideal model delta sigma weight residual 108.06 112.47 -4.41 1.28e+00 6.10e-01 1.19e+01 ... (remaining 25009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 5124 16.70 - 33.40: 366 33.40 - 50.09: 98 50.09 - 66.79: 18 66.79 - 83.49: 7 Dihedral angle restraints: 5613 sinusoidal: 2503 harmonic: 3110 Sorted by residual: dihedral pdb=" CA ASP B 146 " pdb=" C ASP B 146 " pdb=" N ILE B 147 " pdb=" CA ILE B 147 " ideal model delta harmonic sigma weight residual -180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA SER A 434 " pdb=" C SER A 434 " pdb=" N GLU A 435 " pdb=" CA GLU A 435 " ideal model delta harmonic sigma weight residual 180.00 149.18 30.82 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA ILE A 530 " pdb=" C ILE A 530 " pdb=" N ASP A 531 " pdb=" CA ASP A 531 " ideal model delta harmonic sigma weight residual 180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 5610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 657 0.043 - 0.086: 299 0.086 - 0.128: 114 0.128 - 0.171: 14 0.171 - 0.214: 3 Chirality restraints: 1087 Sorted by residual: chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR A 194 " pdb=" CA THR A 194 " pdb=" OG1 THR A 194 " pdb=" CG2 THR A 194 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA ASP A 562 " pdb=" N ASP A 562 " pdb=" C ASP A 562 " pdb=" CB ASP A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 1084 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 602 " -0.013 2.00e-02 2.50e+03 2.88e-02 2.48e+01 pdb=" CG PHE A 602 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 602 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 602 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 602 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 602 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 602 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 602 " 0.062 2.00e-02 2.50e+03 pdb=" HD2 PHE A 602 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE A 602 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE A 602 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 602 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 509 " -0.008 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" CG PHE A 509 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 509 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 509 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 509 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 509 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 509 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 PHE A 509 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 509 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 509 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 509 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 560 " 0.001 2.00e-02 2.50e+03 1.49e-02 6.65e+00 pdb=" CG TYR A 560 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 560 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 560 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 560 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 560 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 560 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 560 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 560 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR A 560 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TYR A 560 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 TYR A 560 " 0.009 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 85 1.87 - 2.55: 12944 2.55 - 3.23: 41723 3.23 - 3.92: 54010 3.92 - 4.60: 87578 Nonbonded interactions: 196340 Sorted by model distance: nonbonded pdb=" HG SER B 144 " pdb=" OD1 ASP B 146 " model vdw 1.186 1.850 nonbonded pdb=" OE1 GLU B 28 " pdb=" HG SER B 57 " model vdw 1.362 1.850 nonbonded pdb=" HG SER B 185 " pdb=" HE1 TRP B 195 " model vdw 1.383 2.100 nonbonded pdb=" HG SER B 142 " pdb=" HE1 TRP B 152 " model vdw 1.455 2.100 nonbonded pdb=" OD1 ASP A 442 " pdb=" HH TYR A 613 " model vdw 1.532 1.850 ... (remaining 196335 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: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 4438 2.51 5 N 1200 2.21 5 O 1301 1.98 5 H 6716 0.53 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=0.50 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: 2.950 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: 0.190 Extract box with map and model: 12.280 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.110 Process input model: 45.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.100 7152 Z= 0.608 Angle : 0.901 7.540 9747 Z= 0.492 Chirality : 0.054 0.214 1087 Planarity : 0.005 0.063 1262 Dihedral : 13.496 83.492 2548 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.30 % Favored : 96.36 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.50 (0.26), residues: 879 helix: -3.31 (0.25), residues: 177 sheet: -0.55 (0.31), residues: 279 loop : -1.60 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.4742 time to fit residues: 137.6842 Evaluate side-chains 173 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 141 HIS A 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 7152 Z= 0.244 Angle : 0.656 6.229 9747 Z= 0.354 Chirality : 0.047 0.150 1087 Planarity : 0.005 0.047 1262 Dihedral : 6.127 24.600 954 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.19 % Favored : 96.59 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.91 (0.26), residues: 879 helix: -1.70 (0.32), residues: 187 sheet: -0.58 (0.30), residues: 271 loop : -1.44 (0.29), residues: 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 194 average time/residue: 0.4473 time to fit residues: 112.9309 Evaluate side-chains 188 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1654 time to fit residues: 5.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 0.0060 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 263 GLN A 289 GLN A 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7152 Z= 0.227 Angle : 0.589 5.988 9747 Z= 0.314 Chirality : 0.045 0.147 1087 Planarity : 0.005 0.085 1262 Dihedral : 5.640 24.374 954 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.19 % Favored : 96.59 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.49 (0.28), residues: 879 helix: -0.82 (0.34), residues: 191 sheet: -0.64 (0.31), residues: 272 loop : -1.21 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 194 average time/residue: 0.4814 time to fit residues: 122.7219 Evaluate side-chains 178 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1615 time to fit residues: 2.2583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 7152 Z= 0.305 Angle : 0.604 5.824 9747 Z= 0.324 Chirality : 0.046 0.152 1087 Planarity : 0.005 0.043 1262 Dihedral : 5.595 23.874 954 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.11 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.57 (0.27), residues: 879 helix: -0.60 (0.34), residues: 190 sheet: -0.78 (0.31), residues: 270 loop : -1.35 (0.30), residues: 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 186 average time/residue: 0.4701 time to fit residues: 112.4383 Evaluate side-chains 178 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.199 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1872 time to fit residues: 3.4340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 7152 Z= 0.360 Angle : 0.613 5.663 9747 Z= 0.329 Chirality : 0.046 0.151 1087 Planarity : 0.005 0.040 1262 Dihedral : 5.622 25.364 954 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.43 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.78 (0.27), residues: 879 helix: -0.54 (0.34), residues: 190 sheet: -0.96 (0.31), residues: 268 loop : -1.56 (0.29), residues: 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 185 average time/residue: 0.4685 time to fit residues: 112.3795 Evaluate side-chains 188 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.197 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1792 time to fit residues: 4.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7152 Z= 0.249 Angle : 0.573 5.512 9747 Z= 0.305 Chirality : 0.045 0.147 1087 Planarity : 0.005 0.057 1262 Dihedral : 5.424 24.994 954 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.01 % Favored : 94.77 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.60 (0.27), residues: 879 helix: -0.19 (0.34), residues: 190 sheet: -0.97 (0.31), residues: 268 loop : -1.46 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 179 average time/residue: 0.4648 time to fit residues: 109.0112 Evaluate side-chains 178 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.034 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2022 time to fit residues: 2.4339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7152 Z= 0.230 Angle : 0.560 5.530 9747 Z= 0.296 Chirality : 0.044 0.147 1087 Planarity : 0.005 0.057 1262 Dihedral : 5.259 23.391 954 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.01 % Favored : 94.77 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.40 (0.27), residues: 879 helix: 0.19 (0.35), residues: 191 sheet: -0.94 (0.31), residues: 267 loop : -1.38 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 187 average time/residue: 0.4905 time to fit residues: 116.8166 Evaluate side-chains 179 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 0.997 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1819 time to fit residues: 2.5774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7152 Z= 0.202 Angle : 0.551 5.514 9747 Z= 0.291 Chirality : 0.044 0.144 1087 Planarity : 0.004 0.053 1262 Dihedral : 5.152 23.696 954 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.32 % Favored : 95.45 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.26 (0.28), residues: 879 helix: 0.47 (0.36), residues: 191 sheet: -0.93 (0.31), residues: 267 loop : -1.33 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.4920 time to fit residues: 115.6245 Evaluate side-chains 182 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.177 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2049 time to fit residues: 2.8588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7152 Z= 0.190 Angle : 0.537 5.515 9747 Z= 0.283 Chirality : 0.044 0.140 1087 Planarity : 0.004 0.052 1262 Dihedral : 5.020 23.421 954 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.21 % Favored : 95.56 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -1.09 (0.28), residues: 879 helix: 0.78 (0.37), residues: 190 sheet: -0.91 (0.31), residues: 267 loop : -1.25 (0.30), residues: 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 179 average time/residue: 0.4764 time to fit residues: 109.7970 Evaluate side-chains 177 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.109 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1877 time to fit residues: 2.0496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7152 Z= 0.181 Angle : 0.534 5.517 9747 Z= 0.282 Chirality : 0.044 0.140 1087 Planarity : 0.005 0.068 1262 Dihedral : 4.957 22.752 954 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.21 % Favored : 95.56 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -0.98 (0.28), residues: 879 helix: 0.93 (0.37), residues: 191 sheet: -0.87 (0.31), residues: 262 loop : -1.19 (0.30), residues: 426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 148 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue ILE 530 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 179 average time/residue: 0.4743 time to fit residues: 110.0053 Evaluate side-chains 180 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 0.970 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1954 time to fit residues: 2.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0870 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.167320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149262 restraints weight = 28785.682| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.92 r_work: 0.3782 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work: 0.3742 rms_B_bonded: 2.02 restraints_weight: 0.1250 r_work: 0.3715 rms_B_bonded: 2.42 restraints_weight: 0.0625 r_work: 0.3678 rms_B_bonded: 3.03 restraints_weight: 0.0312 r_work: 0.3628 rms_B_bonded: 3.95 restraints_weight: 0.0156 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7152 Z= 0.158 Angle : 0.526 5.479 9747 Z= 0.275 Chirality : 0.044 0.141 1087 Planarity : 0.005 0.063 1262 Dihedral : 4.836 21.981 954 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.98 % Favored : 95.90 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.62 % 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: -0.85 (0.28), residues: 879 helix: 1.18 (0.38), residues: 190 sheet: -0.82 (0.31), residues: 260 loop : -1.15 (0.30), residues: 429 =============================================================================== Job complete usr+sys time: 3951.91 seconds wall clock time: 70 minutes 27.47 seconds (4227.47 seconds total)