Starting phenix.real_space_refine on Fri Mar 15 17:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kup_9579/03_2024/6kup_9579_neut.pdb" } resolution = 4.3 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 109 5.16 5 C 7703 2.51 5 N 2092 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 6.34, per 1000 atoms: 0.52 Number of scatterers: 12254 At special positions: 0 Unit cell: (111.52, 110.16, 110.16, 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 109 16.00 P 23 15.00 O 2327 8.00 N 2092 7.00 C 7703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 48.0% alpha, 7.7% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.743A pdb=" N ALA A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.720A pdb=" N THR A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.100A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.749A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.049A pdb=" N ASP A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.136A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.591A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.799A pdb=" N CYS A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.700A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.796A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.997A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.618A pdb=" N GLU B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.645A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.534A pdb=" N CYS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.772A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.873A pdb=" N CYS B 314 " --> pdb=" O TRP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 4.042A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.549A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.677A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.646A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 560 removed outlier: 3.512A pdb=" N ALA B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.831A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.577A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.573A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.989A pdb=" N LEU B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.739A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 30 through 37 removed outlier: 3.964A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.553A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.529A pdb=" N THR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.730A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.601A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.674A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.863A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.604A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.830A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.724A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 478 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.561A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA9, first strand: chain 'B' and resid 438 through 443 removed outlier: 4.133A pdb=" N PHE B 448 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.723A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 153 512 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3691 1.34 - 1.46: 2351 1.46 - 1.58: 6278 1.58 - 1.70: 44 1.70 - 1.82: 181 Bond restraints: 12545 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.27e-02 6.20e+03 2.11e+01 bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.371 -0.037 8.40e-03 1.42e+04 1.98e+01 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.25e-02 6.40e+03 6.81e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.428 0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" C LEU A 203 " pdb=" N PRO A 204 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 ... (remaining 12540 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.91: 397 105.91 - 112.99: 6573 112.99 - 120.07: 4761 120.07 - 127.15: 5053 127.15 - 134.24: 178 Bond angle restraints: 16962 Sorted by residual: angle pdb=" C LEU B 540 " pdb=" N SER B 541 " pdb=" CA SER B 541 " ideal model delta sigma weight residual 120.51 127.61 -7.10 1.45e+00 4.76e-01 2.40e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.69 -5.12 1.25e+00 6.40e-01 1.68e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" N ILE C 159 " pdb=" CA ILE C 159 " pdb=" C ILE C 159 " ideal model delta sigma weight residual 111.62 108.63 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" C TRP A 357 " pdb=" N GLN A 358 " pdb=" CA GLN A 358 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 ... (remaining 16957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 7253 15.20 - 30.40: 309 30.40 - 45.60: 102 45.60 - 60.80: 29 60.80 - 76.01: 27 Dihedral angle restraints: 7720 sinusoidal: 3460 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR B 328 " pdb=" C THR B 328 " pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1412 0.054 - 0.109: 369 0.109 - 0.163: 65 0.163 - 0.217: 6 0.217 - 0.272: 3 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE C 231 " pdb=" CA ILE C 231 " pdb=" CG1 ILE C 231 " pdb=" CG2 ILE C 231 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 155 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO C 156 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 342 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 343 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 731 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C ILE B 731 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE B 731 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1933 2.76 - 3.30: 11010 3.30 - 3.83: 19001 3.83 - 4.37: 22663 4.37 - 4.90: 38410 Nonbonded interactions: 93017 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.227 2.520 nonbonded pdb=" O LEU B 324 " pdb=" OG1 THR B 328 " model vdw 2.296 2.440 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.297 2.440 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.308 2.440 nonbonded pdb=" O VAL B 341 " pdb=" OG1 THR B 344 " model vdw 2.313 2.440 ... (remaining 93012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 1.910 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.004 0.058 12545 Z= 0.262 Angle : 0.809 8.248 16962 Z= 0.452 Chirality : 0.050 0.272 1855 Planarity : 0.006 0.069 2070 Dihedral : 11.438 76.006 4954 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.16), residues: 1441 helix: -3.42 (0.12), residues: 647 sheet: -1.84 (0.52), residues: 91 loop : -3.28 (0.19), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 386 HIS 0.007 0.002 HIS B 606 PHE 0.026 0.002 PHE B 726 TYR 0.018 0.002 TYR A 549 ARG 0.007 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 566 time to evaluate : 1.391 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: A 271 TRP cc_start: 0.7767 (t-100) cc_final: 0.7100 (t-100) REVERT: A 278 ASP cc_start: 0.8685 (t0) cc_final: 0.8421 (t0) REVERT: A 288 LEU cc_start: 0.9683 (tp) cc_final: 0.9456 (tt) REVERT: A 364 GLU cc_start: 0.8341 (mp0) cc_final: 0.8054 (mp0) REVERT: A 382 PHE cc_start: 0.7765 (t80) cc_final: 0.7121 (t80) REVERT: A 386 TRP cc_start: 0.8882 (t-100) cc_final: 0.8254 (t-100) REVERT: A 453 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7672 (tp30) REVERT: A 495 ASP cc_start: 0.8666 (m-30) cc_final: 0.8175 (m-30) REVERT: A 498 TYR cc_start: 0.8407 (p90) cc_final: 0.8098 (p90) REVERT: A 547 PHE cc_start: 0.9005 (m-80) cc_final: 0.8558 (m-10) REVERT: A 555 MET cc_start: 0.8238 (mmm) cc_final: 0.7758 (mmm) REVERT: A 562 TRP cc_start: 0.7924 (m100) cc_final: 0.7213 (m100) REVERT: A 578 GLU cc_start: 0.8803 (tt0) cc_final: 0.8427 (tt0) REVERT: A 600 LYS cc_start: 0.9278 (tppt) cc_final: 0.8777 (tptp) REVERT: A 601 ARG cc_start: 0.8753 (mmt180) cc_final: 0.8531 (mmm160) REVERT: A 639 ASP cc_start: 0.7436 (m-30) cc_final: 0.6536 (m-30) REVERT: A 650 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8328 (mtmt) REVERT: A 661 ASP cc_start: 0.7648 (t0) cc_final: 0.7441 (t0) REVERT: A 684 ASN cc_start: 0.9318 (t0) cc_final: 0.9100 (t0) REVERT: B 10 LEU cc_start: 0.9528 (mt) cc_final: 0.9275 (tt) REVERT: B 45 ARG cc_start: 0.8557 (ttp-170) cc_final: 0.8005 (ttp-170) REVERT: B 52 THR cc_start: 0.8465 (t) cc_final: 0.8185 (t) REVERT: B 85 VAL cc_start: 0.9349 (t) cc_final: 0.8883 (t) REVERT: B 147 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8248 (mm-40) REVERT: B 151 ASP cc_start: 0.8473 (t0) cc_final: 0.7640 (t70) REVERT: B 155 GLU cc_start: 0.7725 (tt0) cc_final: 0.7412 (pt0) REVERT: B 182 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7682 (mtmm) REVERT: B 234 GLU cc_start: 0.7109 (tt0) cc_final: 0.6434 (pm20) REVERT: B 237 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8283 (mptt) REVERT: B 255 LYS cc_start: 0.8564 (tptt) cc_final: 0.8184 (tptt) REVERT: B 311 TRP cc_start: 0.9365 (t-100) cc_final: 0.9082 (t-100) REVERT: B 336 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8430 (mmtp) REVERT: B 389 LEU cc_start: 0.9390 (mt) cc_final: 0.9164 (tp) REVERT: B 410 MET cc_start: 0.5922 (mtp) cc_final: 0.5690 (mtt) REVERT: B 541 SER cc_start: 0.8831 (p) cc_final: 0.8033 (p) REVERT: B 576 ILE cc_start: 0.9376 (mt) cc_final: 0.8946 (tp) REVERT: B 578 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7006 (ptm-80) REVERT: B 610 GLU cc_start: 0.8754 (mp0) cc_final: 0.7889 (pm20) REVERT: B 612 LEU cc_start: 0.8521 (tp) cc_final: 0.7929 (tp) REVERT: B 627 ASN cc_start: 0.8756 (t0) cc_final: 0.8426 (t0) REVERT: B 689 CYS cc_start: 0.8548 (m) cc_final: 0.8253 (m) REVERT: B 736 TYR cc_start: 0.8102 (t80) cc_final: 0.6475 (t80) REVERT: C 55 MET cc_start: 0.8368 (mmm) cc_final: 0.8087 (mmm) REVERT: C 85 LYS cc_start: 0.5817 (mmtm) cc_final: 0.4829 (ptpt) REVERT: C 96 LEU cc_start: 0.8227 (mt) cc_final: 0.7921 (mt) REVERT: C 102 ILE cc_start: 0.8970 (mt) cc_final: 0.8578 (mm) REVERT: C 213 MET cc_start: 0.8486 (ptm) cc_final: 0.8167 (ppp) REVERT: C 218 PHE cc_start: 0.7928 (m-10) cc_final: 0.6825 (m-80) REVERT: C 247 TRP cc_start: 0.8394 (p-90) cc_final: 0.7657 (p90) outliers start: 2 outliers final: 0 residues processed: 566 average time/residue: 0.2967 time to fit residues: 226.9836 Evaluate side-chains 356 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 277 HIS A 560 ASN A 640 ASN B 70 ASN B 147 GLN B 477 ASN B 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12545 Z= 0.174 Angle : 0.610 12.649 16962 Z= 0.313 Chirality : 0.041 0.157 1855 Planarity : 0.005 0.055 2070 Dihedral : 11.494 74.266 1924 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1441 helix: -0.97 (0.18), residues: 655 sheet: -1.45 (0.53), residues: 101 loop : -2.95 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 386 HIS 0.004 0.001 HIS A 451 PHE 0.027 0.001 PHE B 108 TYR 0.031 0.002 TYR B 736 ARG 0.005 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 1.663 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: A 271 TRP cc_start: 0.7659 (t-100) cc_final: 0.7045 (t-100) REVERT: A 315 TYR cc_start: 0.8264 (m-80) cc_final: 0.7908 (m-80) REVERT: A 386 TRP cc_start: 0.8893 (t-100) cc_final: 0.7865 (t-100) REVERT: A 390 MET cc_start: 0.8714 (ptm) cc_final: 0.7612 (ttm) REVERT: A 453 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7921 (tp30) REVERT: A 498 TYR cc_start: 0.7546 (p90) cc_final: 0.6541 (p90) REVERT: A 547 PHE cc_start: 0.9024 (m-80) cc_final: 0.8461 (m-10) REVERT: A 555 MET cc_start: 0.8464 (mmm) cc_final: 0.8224 (mmm) REVERT: A 558 LEU cc_start: 0.8965 (tt) cc_final: 0.8692 (tt) REVERT: A 643 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7616 (mm-30) REVERT: A 654 MET cc_start: 0.9014 (tpp) cc_final: 0.8557 (tpp) REVERT: A 684 ASN cc_start: 0.9253 (t0) cc_final: 0.8492 (m-40) REVERT: B 2 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 52 THR cc_start: 0.8404 (t) cc_final: 0.8174 (t) REVERT: B 85 VAL cc_start: 0.9277 (t) cc_final: 0.9054 (t) REVERT: B 90 MET cc_start: 0.9213 (ptm) cc_final: 0.8720 (ptm) REVERT: B 92 SER cc_start: 0.9372 (m) cc_final: 0.9153 (p) REVERT: B 133 ASP cc_start: 0.8183 (t70) cc_final: 0.7849 (m-30) REVERT: B 151 ASP cc_start: 0.8467 (t0) cc_final: 0.8070 (t70) REVERT: B 174 GLU cc_start: 0.8689 (tt0) cc_final: 0.8017 (tt0) REVERT: B 234 GLU cc_start: 0.6950 (tt0) cc_final: 0.6121 (pm20) REVERT: B 237 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8230 (mptt) REVERT: B 250 ILE cc_start: 0.8805 (mt) cc_final: 0.8553 (mp) REVERT: B 255 LYS cc_start: 0.8770 (tptt) cc_final: 0.8400 (tptt) REVERT: B 258 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 270 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7109 (mp0) REVERT: B 312 ASN cc_start: 0.8961 (m-40) cc_final: 0.8309 (m-40) REVERT: B 408 MET cc_start: 0.6732 (ttm) cc_final: 0.5976 (ttp) REVERT: B 453 ILE cc_start: 0.9146 (pt) cc_final: 0.8840 (tp) REVERT: B 460 MET cc_start: 0.8669 (tpp) cc_final: 0.8261 (tpp) REVERT: B 461 GLU cc_start: 0.8393 (pt0) cc_final: 0.8054 (pt0) REVERT: B 528 MET cc_start: 0.8779 (mtm) cc_final: 0.8323 (mtp) REVERT: B 560 TYR cc_start: 0.8676 (m-10) cc_final: 0.8341 (m-10) REVERT: B 578 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7095 (ptm-80) REVERT: B 587 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7691 (mmmt) REVERT: B 591 LEU cc_start: 0.9039 (tp) cc_final: 0.8672 (tp) REVERT: B 681 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 714 ILE cc_start: 0.8718 (mm) cc_final: 0.8483 (mm) REVERT: C 51 MET cc_start: 0.8968 (tpp) cc_final: 0.8743 (tpp) REVERT: C 55 MET cc_start: 0.8465 (mmm) cc_final: 0.8207 (mmm) REVERT: C 85 LYS cc_start: 0.5557 (mmtm) cc_final: 0.4276 (ptpt) REVERT: C 213 MET cc_start: 0.9115 (ptm) cc_final: 0.8634 (ppp) REVERT: C 214 ILE cc_start: 0.9276 (mt) cc_final: 0.8922 (mt) REVERT: C 218 PHE cc_start: 0.8222 (m-10) cc_final: 0.6973 (m-80) REVERT: C 242 LEU cc_start: 0.8526 (tt) cc_final: 0.8296 (tt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2757 time to fit residues: 158.8372 Evaluate side-chains 326 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN A 606 HIS ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12545 Z= 0.259 Angle : 0.626 9.093 16962 Z= 0.326 Chirality : 0.042 0.144 1855 Planarity : 0.005 0.060 2070 Dihedral : 11.428 74.289 1924 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 0.39 % Allowed : 2.57 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1441 helix: -0.06 (0.20), residues: 662 sheet: -1.22 (0.52), residues: 105 loop : -2.82 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 386 HIS 0.005 0.001 HIS C 216 PHE 0.017 0.002 PHE A 481 TYR 0.014 0.002 TYR A 205 ARG 0.005 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 364 time to evaluate : 1.298 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: A 188 TYR cc_start: 0.8961 (t80) cc_final: 0.8712 (t80) REVERT: A 193 PHE cc_start: 0.8928 (t80) cc_final: 0.8711 (t80) REVERT: A 315 TYR cc_start: 0.8364 (m-80) cc_final: 0.8125 (m-80) REVERT: A 332 GLU cc_start: 0.7836 (pt0) cc_final: 0.7054 (pm20) REVERT: A 364 GLU cc_start: 0.8455 (mp0) cc_final: 0.8144 (mp0) REVERT: A 406 MET cc_start: 0.8296 (tpp) cc_final: 0.7541 (mtt) REVERT: A 428 GLU cc_start: 0.8238 (tp30) cc_final: 0.7492 (tp30) REVERT: A 453 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7638 (tp30) REVERT: A 475 GLU cc_start: 0.7774 (pp20) cc_final: 0.7556 (pp20) REVERT: A 526 VAL cc_start: 0.9305 (t) cc_final: 0.9094 (t) REVERT: A 547 PHE cc_start: 0.8962 (m-80) cc_final: 0.8597 (m-80) REVERT: A 557 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8061 (ttmt) REVERT: A 643 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7720 (mm-30) REVERT: A 649 GLN cc_start: 0.8613 (pt0) cc_final: 0.8338 (pt0) REVERT: A 654 MET cc_start: 0.8904 (tpp) cc_final: 0.8376 (tpp) REVERT: B 1 MET cc_start: 0.7216 (ttp) cc_final: 0.6987 (tmm) REVERT: B 78 LEU cc_start: 0.8772 (tp) cc_final: 0.8458 (tp) REVERT: B 80 LYS cc_start: 0.9263 (mmmm) cc_final: 0.8853 (mmtm) REVERT: B 90 MET cc_start: 0.9143 (ptm) cc_final: 0.8918 (ptm) REVERT: B 92 SER cc_start: 0.9480 (m) cc_final: 0.9220 (p) REVERT: B 133 ASP cc_start: 0.8430 (t70) cc_final: 0.8195 (m-30) REVERT: B 151 ASP cc_start: 0.8479 (t0) cc_final: 0.8041 (t0) REVERT: B 174 GLU cc_start: 0.8762 (tt0) cc_final: 0.8023 (tt0) REVERT: B 183 PHE cc_start: 0.8666 (p90) cc_final: 0.8055 (p90) REVERT: B 234 GLU cc_start: 0.7062 (tt0) cc_final: 0.6242 (pm20) REVERT: B 237 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8386 (mptt) REVERT: B 250 ILE cc_start: 0.8971 (mt) cc_final: 0.8701 (mp) REVERT: B 255 LYS cc_start: 0.8806 (tptt) cc_final: 0.8279 (tptt) REVERT: B 258 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7033 (mt-10) REVERT: B 312 ASN cc_start: 0.9005 (m-40) cc_final: 0.8345 (m-40) REVERT: B 320 TYR cc_start: 0.8612 (m-10) cc_final: 0.8362 (m-10) REVERT: B 339 CYS cc_start: 0.8529 (m) cc_final: 0.8228 (m) REVERT: B 375 MET cc_start: 0.8980 (mtp) cc_final: 0.8673 (mtp) REVERT: B 383 ASN cc_start: 0.8330 (m110) cc_final: 0.8125 (m110) REVERT: B 389 LEU cc_start: 0.9184 (tp) cc_final: 0.8933 (tt) REVERT: B 408 MET cc_start: 0.7200 (ttm) cc_final: 0.6743 (ttp) REVERT: B 423 MET cc_start: 0.9646 (mtp) cc_final: 0.9209 (mtp) REVERT: B 462 MET cc_start: 0.8666 (mtm) cc_final: 0.8404 (mtp) REVERT: B 490 LEU cc_start: 0.9186 (tp) cc_final: 0.8684 (tp) REVERT: B 496 MET cc_start: 0.8833 (mtp) cc_final: 0.8091 (mtt) REVERT: B 547 MET cc_start: 0.9030 (tpp) cc_final: 0.8536 (ttm) REVERT: B 578 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7124 (ptm-80) REVERT: B 587 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8212 (mmmt) REVERT: C 32 TYR cc_start: 0.8115 (t80) cc_final: 0.7662 (t80) REVERT: C 55 MET cc_start: 0.8745 (mmm) cc_final: 0.8531 (mmm) REVERT: C 85 LYS cc_start: 0.6017 (mmtm) cc_final: 0.4805 (ptpt) REVERT: C 102 ILE cc_start: 0.9064 (mt) cc_final: 0.8855 (mp) REVERT: C 103 THR cc_start: 0.9121 (p) cc_final: 0.8767 (t) REVERT: C 160 LYS cc_start: 0.9163 (tttt) cc_final: 0.8915 (tttm) REVERT: C 213 MET cc_start: 0.9140 (ptm) cc_final: 0.8671 (ppp) REVERT: C 218 PHE cc_start: 0.8129 (m-10) cc_final: 0.6960 (m-80) outliers start: 5 outliers final: 3 residues processed: 366 average time/residue: 0.2559 time to fit residues: 131.3579 Evaluate side-chains 296 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 477 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12545 Z= 0.220 Angle : 0.604 11.159 16962 Z= 0.309 Chirality : 0.042 0.172 1855 Planarity : 0.004 0.056 2070 Dihedral : 11.311 74.042 1924 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1441 helix: 0.38 (0.20), residues: 646 sheet: -1.14 (0.53), residues: 104 loop : -2.69 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 83 HIS 0.004 0.001 HIS C 216 PHE 0.024 0.001 PHE B 108 TYR 0.016 0.001 TYR A 208 ARG 0.005 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.444 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: A 193 PHE cc_start: 0.8961 (t80) cc_final: 0.8619 (t80) REVERT: A 235 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8276 (tpm170) REVERT: A 332 GLU cc_start: 0.7859 (pt0) cc_final: 0.6988 (pm20) REVERT: A 364 GLU cc_start: 0.8506 (mp0) cc_final: 0.8147 (mp0) REVERT: A 406 MET cc_start: 0.8319 (tpp) cc_final: 0.7505 (mtt) REVERT: A 428 GLU cc_start: 0.8308 (tp30) cc_final: 0.7503 (tp30) REVERT: A 453 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7637 (tp30) REVERT: A 475 GLU cc_start: 0.8007 (pp20) cc_final: 0.7727 (pp20) REVERT: A 547 PHE cc_start: 0.9086 (m-80) cc_final: 0.8856 (m-80) REVERT: A 557 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8127 (ttmt) REVERT: A 643 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7983 (mm-30) REVERT: A 654 MET cc_start: 0.8880 (tpp) cc_final: 0.8528 (tpp) REVERT: A 684 ASN cc_start: 0.9340 (t0) cc_final: 0.8707 (m110) REVERT: B 2 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6595 (mp0) REVERT: B 4 ASN cc_start: 0.9271 (t0) cc_final: 0.8810 (t0) REVERT: B 7 LEU cc_start: 0.9472 (mt) cc_final: 0.9247 (mt) REVERT: B 78 LEU cc_start: 0.8768 (tp) cc_final: 0.8490 (tp) REVERT: B 80 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8809 (mmtm) REVERT: B 87 ILE cc_start: 0.9247 (pt) cc_final: 0.9041 (pt) REVERT: B 92 SER cc_start: 0.9411 (m) cc_final: 0.9109 (p) REVERT: B 112 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8461 (mp0) REVERT: B 151 ASP cc_start: 0.8285 (t0) cc_final: 0.7910 (t0) REVERT: B 174 GLU cc_start: 0.8817 (tt0) cc_final: 0.8135 (tt0) REVERT: B 234 GLU cc_start: 0.7054 (tt0) cc_final: 0.6597 (pm20) REVERT: B 237 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8438 (mptt) REVERT: B 250 ILE cc_start: 0.9036 (mt) cc_final: 0.8789 (mp) REVERT: B 255 LYS cc_start: 0.8788 (tptt) cc_final: 0.8301 (tptt) REVERT: B 258 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 320 TYR cc_start: 0.8512 (m-10) cc_final: 0.8204 (m-10) REVERT: B 339 CYS cc_start: 0.8657 (m) cc_final: 0.8406 (p) REVERT: B 349 LYS cc_start: 0.9141 (pttm) cc_final: 0.8872 (ptpp) REVERT: B 375 MET cc_start: 0.8934 (mtp) cc_final: 0.8614 (mtp) REVERT: B 389 LEU cc_start: 0.9108 (tp) cc_final: 0.8819 (tt) REVERT: B 408 MET cc_start: 0.7599 (ttm) cc_final: 0.7247 (ttp) REVERT: B 423 MET cc_start: 0.9565 (mtp) cc_final: 0.9257 (mtp) REVERT: B 462 MET cc_start: 0.8588 (mtm) cc_final: 0.8185 (mtp) REVERT: B 490 LEU cc_start: 0.9107 (tp) cc_final: 0.8598 (tp) REVERT: B 496 MET cc_start: 0.8821 (mtp) cc_final: 0.8534 (mtt) REVERT: B 528 MET cc_start: 0.8767 (mtp) cc_final: 0.8397 (mtt) REVERT: B 578 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7495 (mtm180) REVERT: B 587 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8316 (tppt) REVERT: B 599 MET cc_start: 0.8924 (tpp) cc_final: 0.8132 (tpt) REVERT: B 611 ILE cc_start: 0.8373 (mt) cc_final: 0.7979 (mt) REVERT: B 749 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6981 (tm-30) REVERT: C 51 MET cc_start: 0.9026 (tpp) cc_final: 0.8809 (tpp) REVERT: C 55 MET cc_start: 0.8746 (mmm) cc_final: 0.8311 (mmm) REVERT: C 81 ASP cc_start: 0.7663 (t0) cc_final: 0.7283 (t0) REVERT: C 85 LYS cc_start: 0.6553 (mmtm) cc_final: 0.6027 (mmmm) REVERT: C 102 ILE cc_start: 0.9201 (mt) cc_final: 0.8988 (mp) REVERT: C 103 THR cc_start: 0.9082 (p) cc_final: 0.8747 (t) REVERT: C 160 LYS cc_start: 0.9067 (tttt) cc_final: 0.8800 (tttm) REVERT: C 213 MET cc_start: 0.9128 (ptm) cc_final: 0.8740 (ppp) REVERT: C 218 PHE cc_start: 0.8344 (m-10) cc_final: 0.7356 (m-80) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2619 time to fit residues: 129.6990 Evaluate side-chains 289 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12545 Z= 0.289 Angle : 0.648 9.348 16962 Z= 0.336 Chirality : 0.043 0.142 1855 Planarity : 0.004 0.063 2070 Dihedral : 11.378 74.117 1924 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.54 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1441 helix: 0.38 (0.20), residues: 653 sheet: -1.25 (0.50), residues: 110 loop : -2.78 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 38 HIS 0.004 0.001 HIS A 210 PHE 0.021 0.002 PHE B 108 TYR 0.020 0.002 TYR B 736 ARG 0.005 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.487 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: A 193 PHE cc_start: 0.9050 (t80) cc_final: 0.8546 (t80) REVERT: A 290 ASP cc_start: 0.8072 (m-30) cc_final: 0.7675 (m-30) REVERT: A 332 GLU cc_start: 0.7681 (pt0) cc_final: 0.7141 (pm20) REVERT: A 340 ASP cc_start: 0.8776 (t70) cc_final: 0.8540 (t70) REVERT: A 364 GLU cc_start: 0.8543 (mp0) cc_final: 0.8268 (mp0) REVERT: A 406 MET cc_start: 0.8596 (tpp) cc_final: 0.7590 (mtt) REVERT: A 409 MET cc_start: 0.8965 (mmm) cc_final: 0.8524 (mmm) REVERT: A 428 GLU cc_start: 0.8273 (tp30) cc_final: 0.7467 (tp30) REVERT: A 453 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7501 (tp30) REVERT: A 475 GLU cc_start: 0.8175 (pp20) cc_final: 0.7884 (pp20) REVERT: A 570 LEU cc_start: 0.8640 (mp) cc_final: 0.7964 (mp) REVERT: A 643 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8160 (mm-30) REVERT: A 654 MET cc_start: 0.8847 (tpp) cc_final: 0.8395 (tpp) REVERT: B 4 ASN cc_start: 0.9326 (t0) cc_final: 0.8846 (t0) REVERT: B 7 LEU cc_start: 0.9629 (mt) cc_final: 0.9230 (mt) REVERT: B 78 LEU cc_start: 0.8899 (tp) cc_final: 0.8564 (tp) REVERT: B 80 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8721 (mmtm) REVERT: B 90 MET cc_start: 0.9076 (ptm) cc_final: 0.8829 (ptm) REVERT: B 92 SER cc_start: 0.9392 (m) cc_final: 0.9109 (p) REVERT: B 112 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8230 (mp0) REVERT: B 138 ARG cc_start: 0.7369 (ttp-170) cc_final: 0.7091 (ttp-110) REVERT: B 147 GLN cc_start: 0.8683 (tp40) cc_final: 0.8178 (tm-30) REVERT: B 155 GLU cc_start: 0.8734 (tt0) cc_final: 0.8407 (pt0) REVERT: B 174 GLU cc_start: 0.8889 (tt0) cc_final: 0.8511 (tm-30) REVERT: B 234 GLU cc_start: 0.7347 (tt0) cc_final: 0.7023 (pm20) REVERT: B 237 LYS cc_start: 0.9279 (mtpp) cc_final: 0.8477 (mptt) REVERT: B 250 ILE cc_start: 0.9056 (mt) cc_final: 0.8821 (mp) REVERT: B 255 LYS cc_start: 0.8762 (tptt) cc_final: 0.8238 (tptt) REVERT: B 258 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 320 TYR cc_start: 0.8678 (m-10) cc_final: 0.8392 (m-10) REVERT: B 336 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8694 (mttp) REVERT: B 339 CYS cc_start: 0.8711 (m) cc_final: 0.8471 (p) REVERT: B 375 MET cc_start: 0.8986 (mtp) cc_final: 0.8751 (mtp) REVERT: B 397 MET cc_start: 0.8288 (tpp) cc_final: 0.7944 (tpp) REVERT: B 402 CYS cc_start: 0.8554 (t) cc_final: 0.8216 (t) REVERT: B 408 MET cc_start: 0.7646 (ttm) cc_final: 0.7241 (ttp) REVERT: B 423 MET cc_start: 0.9496 (mtp) cc_final: 0.9120 (mtp) REVERT: B 442 LEU cc_start: 0.8874 (tp) cc_final: 0.8278 (tp) REVERT: B 461 GLU cc_start: 0.8351 (pt0) cc_final: 0.8082 (pt0) REVERT: B 462 MET cc_start: 0.8472 (mtm) cc_final: 0.8081 (mtp) REVERT: B 490 LEU cc_start: 0.9160 (tp) cc_final: 0.8664 (tp) REVERT: B 528 MET cc_start: 0.8888 (mtp) cc_final: 0.8516 (mtt) REVERT: B 547 MET cc_start: 0.9019 (tpp) cc_final: 0.8217 (mmm) REVERT: B 578 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7322 (mtm180) REVERT: B 587 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7764 (mmtm) REVERT: B 611 ILE cc_start: 0.8623 (mt) cc_final: 0.8354 (mm) REVERT: B 663 ARG cc_start: 0.6532 (tpp-160) cc_final: 0.5854 (tpp80) REVERT: C 85 LYS cc_start: 0.6304 (mmtm) cc_final: 0.5909 (mmmm) REVERT: C 155 GLN cc_start: 0.8464 (tp40) cc_final: 0.8134 (tp40) REVERT: C 213 MET cc_start: 0.9136 (ptm) cc_final: 0.8724 (ppp) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2564 time to fit residues: 121.2302 Evaluate side-chains 287 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 0.0070 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12545 Z= 0.183 Angle : 0.584 9.651 16962 Z= 0.300 Chirality : 0.041 0.157 1855 Planarity : 0.004 0.067 2070 Dihedral : 11.239 73.752 1924 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.73 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1441 helix: 0.67 (0.21), residues: 649 sheet: -1.28 (0.53), residues: 100 loop : -2.59 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 83 HIS 0.004 0.001 HIS A 490 PHE 0.019 0.001 PHE B 108 TYR 0.014 0.001 TYR C 104 ARG 0.009 0.001 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.722 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: A 193 PHE cc_start: 0.8982 (t80) cc_final: 0.8575 (t80) REVERT: A 235 ARG cc_start: 0.8604 (mmm160) cc_final: 0.7987 (tpm170) REVERT: A 289 TYR cc_start: 0.8459 (m-10) cc_final: 0.6993 (m-10) REVERT: A 290 ASP cc_start: 0.8128 (m-30) cc_final: 0.7744 (m-30) REVERT: A 332 GLU cc_start: 0.7610 (pt0) cc_final: 0.7025 (pm20) REVERT: A 340 ASP cc_start: 0.8753 (t70) cc_final: 0.8529 (t70) REVERT: A 364 GLU cc_start: 0.8425 (mp0) cc_final: 0.8151 (mp0) REVERT: A 406 MET cc_start: 0.8593 (tpp) cc_final: 0.7490 (mtt) REVERT: A 428 GLU cc_start: 0.8365 (tp30) cc_final: 0.7442 (tp30) REVERT: A 442 LYS cc_start: 0.9133 (mttp) cc_final: 0.8853 (mmtm) REVERT: A 453 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 475 GLU cc_start: 0.8296 (pp20) cc_final: 0.7920 (pp20) REVERT: A 570 LEU cc_start: 0.8505 (mp) cc_final: 0.7834 (mt) REVERT: A 633 TYR cc_start: 0.8888 (m-80) cc_final: 0.8411 (m-80) REVERT: A 643 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7962 (mm-30) REVERT: A 653 LEU cc_start: 0.9350 (mp) cc_final: 0.9010 (mp) REVERT: A 654 MET cc_start: 0.8762 (tpp) cc_final: 0.8276 (tpp) REVERT: A 684 ASN cc_start: 0.9311 (t0) cc_final: 0.9007 (t0) REVERT: A 709 PHE cc_start: 0.6944 (t80) cc_final: 0.6618 (t80) REVERT: B 4 ASN cc_start: 0.9205 (t0) cc_final: 0.8800 (t0) REVERT: B 7 LEU cc_start: 0.9598 (mt) cc_final: 0.9219 (mt) REVERT: B 78 LEU cc_start: 0.8879 (tp) cc_final: 0.8583 (tp) REVERT: B 80 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8698 (mmtm) REVERT: B 90 MET cc_start: 0.9071 (ptm) cc_final: 0.8836 (ptm) REVERT: B 92 SER cc_start: 0.9363 (m) cc_final: 0.9060 (p) REVERT: B 138 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.6905 (ttp-110) REVERT: B 140 MET cc_start: 0.7593 (tpp) cc_final: 0.7187 (mmm) REVERT: B 155 GLU cc_start: 0.8676 (tt0) cc_final: 0.8300 (pt0) REVERT: B 174 GLU cc_start: 0.8842 (tt0) cc_final: 0.8458 (tm-30) REVERT: B 234 GLU cc_start: 0.7324 (tt0) cc_final: 0.6976 (pm20) REVERT: B 237 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8566 (mptt) REVERT: B 250 ILE cc_start: 0.9001 (mt) cc_final: 0.8762 (mp) REVERT: B 255 LYS cc_start: 0.8725 (tptt) cc_final: 0.8214 (tptt) REVERT: B 258 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7244 (mt-10) REVERT: B 320 TYR cc_start: 0.8273 (m-10) cc_final: 0.7773 (m-10) REVERT: B 327 ILE cc_start: 0.9468 (mt) cc_final: 0.9260 (tt) REVERT: B 336 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8775 (mttp) REVERT: B 339 CYS cc_start: 0.8830 (m) cc_final: 0.8504 (m) REVERT: B 375 MET cc_start: 0.8962 (mtp) cc_final: 0.8712 (mtp) REVERT: B 397 MET cc_start: 0.8204 (tpp) cc_final: 0.7906 (tpp) REVERT: B 402 CYS cc_start: 0.8624 (t) cc_final: 0.8374 (t) REVERT: B 408 MET cc_start: 0.7824 (ttm) cc_final: 0.7500 (ttp) REVERT: B 423 MET cc_start: 0.9458 (mtp) cc_final: 0.9210 (mtp) REVERT: B 461 GLU cc_start: 0.8305 (pt0) cc_final: 0.8047 (pt0) REVERT: B 462 MET cc_start: 0.8458 (mtm) cc_final: 0.8019 (mtp) REVERT: B 490 LEU cc_start: 0.9032 (tp) cc_final: 0.8542 (tp) REVERT: B 528 MET cc_start: 0.8878 (mtp) cc_final: 0.8466 (mtp) REVERT: B 547 MET cc_start: 0.8808 (tpp) cc_final: 0.8181 (mmm) REVERT: B 578 ARG cc_start: 0.8058 (tpp80) cc_final: 0.7257 (mtm180) REVERT: B 587 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8055 (mmmt) REVERT: B 611 ILE cc_start: 0.8483 (mt) cc_final: 0.8095 (mp) REVERT: C 55 MET cc_start: 0.8717 (mmm) cc_final: 0.8397 (mmm) REVERT: C 85 LYS cc_start: 0.6393 (mmtm) cc_final: 0.5864 (mmmm) REVERT: C 131 ARG cc_start: 0.8620 (mtm110) cc_final: 0.8373 (mtm110) REVERT: C 155 GLN cc_start: 0.8325 (tp40) cc_final: 0.7922 (tp40) REVERT: C 160 LYS cc_start: 0.9041 (tttt) cc_final: 0.8823 (tttm) REVERT: C 170 THR cc_start: 0.7976 (p) cc_final: 0.7473 (p) REVERT: C 171 MET cc_start: 0.8193 (mmt) cc_final: 0.7903 (mmt) REVERT: C 213 MET cc_start: 0.9096 (ptm) cc_final: 0.8702 (ppp) REVERT: C 218 PHE cc_start: 0.8501 (m-10) cc_final: 0.7368 (m-80) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2587 time to fit residues: 123.1580 Evaluate side-chains 300 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 0.0010 chunk 88 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12545 Z= 0.152 Angle : 0.575 8.618 16962 Z= 0.292 Chirality : 0.041 0.158 1855 Planarity : 0.004 0.055 2070 Dihedral : 11.137 73.541 1924 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1441 helix: 0.79 (0.21), residues: 657 sheet: -1.14 (0.54), residues: 100 loop : -2.47 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 134 HIS 0.004 0.001 HIS A 490 PHE 0.019 0.001 PHE B 108 TYR 0.011 0.001 TYR B 49 ARG 0.006 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.391 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: A 193 PHE cc_start: 0.8899 (t80) cc_final: 0.8475 (t80) REVERT: A 240 LEU cc_start: 0.9013 (mt) cc_final: 0.8792 (mt) REVERT: A 340 ASP cc_start: 0.8719 (t70) cc_final: 0.8474 (t70) REVERT: A 406 MET cc_start: 0.8535 (tpp) cc_final: 0.7810 (mtt) REVERT: A 427 LEU cc_start: 0.8835 (tp) cc_final: 0.8621 (tt) REVERT: A 442 LYS cc_start: 0.9147 (mttp) cc_final: 0.8864 (mmtm) REVERT: A 453 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7442 (tp30) REVERT: A 475 GLU cc_start: 0.8322 (pp20) cc_final: 0.7911 (pp20) REVERT: A 517 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8237 (tppt) REVERT: A 557 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8061 (ttmt) REVERT: A 643 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7954 (mm-30) REVERT: A 653 LEU cc_start: 0.9341 (mp) cc_final: 0.9020 (mp) REVERT: A 654 MET cc_start: 0.8677 (tpp) cc_final: 0.8319 (tpp) REVERT: A 669 ASN cc_start: 0.9135 (t0) cc_final: 0.8866 (t0) REVERT: A 684 ASN cc_start: 0.9123 (t0) cc_final: 0.8498 (m110) REVERT: A 709 PHE cc_start: 0.6921 (t80) cc_final: 0.6586 (t80) REVERT: B 2 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6760 (mp0) REVERT: B 4 ASN cc_start: 0.9098 (t0) cc_final: 0.8798 (t0) REVERT: B 7 LEU cc_start: 0.9590 (mt) cc_final: 0.9233 (mt) REVERT: B 65 ARG cc_start: 0.7841 (ttm170) cc_final: 0.6942 (ttm-80) REVERT: B 80 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8601 (mmtm) REVERT: B 87 ILE cc_start: 0.9322 (pt) cc_final: 0.8811 (pt) REVERT: B 90 MET cc_start: 0.9067 (ptm) cc_final: 0.8755 (ptm) REVERT: B 92 SER cc_start: 0.9399 (m) cc_final: 0.9082 (p) REVERT: B 112 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8302 (mp0) REVERT: B 155 GLU cc_start: 0.8710 (tt0) cc_final: 0.8270 (pt0) REVERT: B 174 GLU cc_start: 0.8758 (tt0) cc_final: 0.8107 (tt0) REVERT: B 234 GLU cc_start: 0.7388 (tt0) cc_final: 0.7088 (pt0) REVERT: B 237 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8638 (mptt) REVERT: B 255 LYS cc_start: 0.8736 (tptt) cc_final: 0.8125 (tptt) REVERT: B 258 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 320 TYR cc_start: 0.8101 (m-10) cc_final: 0.7667 (m-10) REVERT: B 339 CYS cc_start: 0.8806 (m) cc_final: 0.8472 (m) REVERT: B 375 MET cc_start: 0.8948 (mtp) cc_final: 0.8710 (mtp) REVERT: B 397 MET cc_start: 0.8153 (tpp) cc_final: 0.7922 (tpp) REVERT: B 402 CYS cc_start: 0.8511 (t) cc_final: 0.8251 (t) REVERT: B 408 MET cc_start: 0.7820 (ttm) cc_final: 0.7595 (ttp) REVERT: B 423 MET cc_start: 0.9460 (mtp) cc_final: 0.9179 (mtp) REVERT: B 442 LEU cc_start: 0.8633 (tp) cc_final: 0.8030 (tp) REVERT: B 462 MET cc_start: 0.8527 (mtm) cc_final: 0.8036 (mtp) REVERT: B 574 MET cc_start: 0.8411 (mmt) cc_final: 0.8038 (mmm) REVERT: B 578 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7033 (ptm160) REVERT: B 587 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7994 (mmmt) REVERT: B 611 ILE cc_start: 0.8360 (mt) cc_final: 0.8035 (mp) REVERT: B 663 ARG cc_start: 0.6363 (tpp-160) cc_final: 0.5830 (tpp-160) REVERT: C 10 GLU cc_start: 0.9087 (mp0) cc_final: 0.8682 (mp0) REVERT: C 51 MET cc_start: 0.9063 (tpp) cc_final: 0.8604 (tpp) REVERT: C 55 MET cc_start: 0.8710 (mmm) cc_final: 0.8339 (mmm) REVERT: C 85 LYS cc_start: 0.6274 (mmtm) cc_final: 0.5856 (mmmm) REVERT: C 160 LYS cc_start: 0.9007 (tttt) cc_final: 0.8783 (tttm) REVERT: C 213 MET cc_start: 0.9083 (ptm) cc_final: 0.8729 (ppp) REVERT: C 218 PHE cc_start: 0.8403 (m-10) cc_final: 0.7407 (m-80) REVERT: C 237 GLU cc_start: 0.7789 (pm20) cc_final: 0.7339 (pm20) REVERT: C 242 LEU cc_start: 0.8931 (tp) cc_final: 0.8718 (tt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2595 time to fit residues: 125.4207 Evaluate side-chains 308 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12545 Z= 0.269 Angle : 0.649 9.813 16962 Z= 0.334 Chirality : 0.043 0.165 1855 Planarity : 0.005 0.067 2070 Dihedral : 11.246 73.809 1924 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1441 helix: 0.53 (0.21), residues: 662 sheet: -1.29 (0.50), residues: 105 loop : -2.58 (0.21), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 134 HIS 0.003 0.001 HIS B 606 PHE 0.020 0.002 PHE C 126 TYR 0.016 0.002 TYR B 692 ARG 0.012 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.578 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: A 193 PHE cc_start: 0.8899 (t80) cc_final: 0.8488 (t80) REVERT: A 289 TYR cc_start: 0.8627 (m-10) cc_final: 0.7205 (m-10) REVERT: A 290 ASP cc_start: 0.8215 (m-30) cc_final: 0.7791 (m-30) REVERT: A 340 ASP cc_start: 0.8751 (t70) cc_final: 0.8519 (t70) REVERT: A 406 MET cc_start: 0.8637 (tpp) cc_final: 0.7878 (mtt) REVERT: A 453 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7475 (tp30) REVERT: A 570 LEU cc_start: 0.8537 (mp) cc_final: 0.7764 (mp) REVERT: A 643 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8028 (mm-30) REVERT: A 654 MET cc_start: 0.8684 (tpp) cc_final: 0.8345 (tpp) REVERT: A 709 PHE cc_start: 0.7130 (t80) cc_final: 0.6757 (t80) REVERT: B 2 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6082 (mp0) REVERT: B 4 ASN cc_start: 0.9249 (t0) cc_final: 0.8851 (t0) REVERT: B 7 LEU cc_start: 0.9693 (mt) cc_final: 0.9285 (mt) REVERT: B 80 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8616 (mmtm) REVERT: B 87 ILE cc_start: 0.9459 (pt) cc_final: 0.9242 (pt) REVERT: B 90 MET cc_start: 0.9055 (ptm) cc_final: 0.8832 (ptm) REVERT: B 92 SER cc_start: 0.9425 (m) cc_final: 0.9085 (p) REVERT: B 112 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8276 (mp0) REVERT: B 138 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.6765 (ttp-110) REVERT: B 140 MET cc_start: 0.7815 (tpp) cc_final: 0.7017 (mmm) REVERT: B 155 GLU cc_start: 0.8820 (tt0) cc_final: 0.8381 (pt0) REVERT: B 174 GLU cc_start: 0.8859 (tt0) cc_final: 0.8429 (tm-30) REVERT: B 234 GLU cc_start: 0.7527 (tt0) cc_final: 0.7326 (pt0) REVERT: B 237 LYS cc_start: 0.9297 (mtpp) cc_final: 0.8709 (mptt) REVERT: B 250 ILE cc_start: 0.9042 (mp) cc_final: 0.8829 (mp) REVERT: B 255 LYS cc_start: 0.8720 (tptt) cc_final: 0.8235 (tptt) REVERT: B 258 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 312 ASN cc_start: 0.8901 (m110) cc_final: 0.8669 (m-40) REVERT: B 320 TYR cc_start: 0.8171 (m-10) cc_final: 0.7798 (m-10) REVERT: B 375 MET cc_start: 0.9004 (mtp) cc_final: 0.8746 (mtp) REVERT: B 408 MET cc_start: 0.7978 (ttm) cc_final: 0.7596 (ttp) REVERT: B 423 MET cc_start: 0.9422 (mtp) cc_final: 0.9151 (mtp) REVERT: B 425 LEU cc_start: 0.9426 (tp) cc_final: 0.9189 (tt) REVERT: B 460 MET cc_start: 0.8724 (tpp) cc_final: 0.8454 (tpp) REVERT: B 462 MET cc_start: 0.8625 (mtm) cc_final: 0.8199 (mtp) REVERT: B 490 LEU cc_start: 0.9079 (tp) cc_final: 0.8521 (tp) REVERT: B 496 MET cc_start: 0.8431 (mtt) cc_final: 0.8223 (mtp) REVERT: B 528 MET cc_start: 0.8792 (mtp) cc_final: 0.8493 (mtt) REVERT: B 547 MET cc_start: 0.8997 (tpp) cc_final: 0.8223 (mmm) REVERT: B 574 MET cc_start: 0.8334 (mmt) cc_final: 0.7961 (mmm) REVERT: B 578 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7230 (mtm180) REVERT: B 587 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8110 (mmmt) REVERT: B 613 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8549 (mmtm) REVERT: B 663 ARG cc_start: 0.6498 (tpp-160) cc_final: 0.5678 (tpp80) REVERT: C 55 MET cc_start: 0.8675 (mmm) cc_final: 0.8143 (mmm) REVERT: C 85 LYS cc_start: 0.6345 (mmtm) cc_final: 0.6067 (mmmm) REVERT: C 160 LYS cc_start: 0.9005 (tttt) cc_final: 0.8766 (tttm) REVERT: C 200 TYR cc_start: 0.6875 (m-80) cc_final: 0.6626 (m-80) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2522 time to fit residues: 117.9980 Evaluate side-chains 285 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0827 > 50: distance: 69 - 137: 13.910 distance: 72 - 134: 11.575 distance: 89 - 91: 21.852 distance: 91 - 92: 18.975 distance: 92 - 93: 14.761 distance: 92 - 95: 15.468 distance: 93 - 94: 55.083 distance: 93 - 99: 16.167 distance: 95 - 96: 14.842 distance: 95 - 97: 33.760 distance: 96 - 98: 31.148 distance: 99 - 100: 7.192 distance: 100 - 101: 39.749 distance: 100 - 103: 28.831 distance: 101 - 102: 22.613 distance: 101 - 110: 29.338 distance: 103 - 104: 10.067 distance: 104 - 105: 6.513 distance: 104 - 106: 14.796 distance: 105 - 107: 42.282 distance: 106 - 108: 29.531 distance: 107 - 109: 17.324 distance: 108 - 109: 28.978 distance: 110 - 111: 26.892 distance: 110 - 116: 17.693 distance: 111 - 114: 21.169 distance: 112 - 113: 40.108 distance: 112 - 117: 22.131 distance: 114 - 115: 36.759 distance: 115 - 116: 20.232 distance: 117 - 118: 36.304 distance: 118 - 121: 8.557 distance: 119 - 120: 19.996 distance: 119 - 125: 19.792 distance: 121 - 122: 36.195 distance: 121 - 123: 36.236 distance: 122 - 124: 17.169 distance: 125 - 126: 12.827 distance: 126 - 127: 11.582 distance: 126 - 129: 15.446 distance: 127 - 128: 17.251 distance: 127 - 134: 12.714 distance: 129 - 130: 35.646 distance: 130 - 131: 23.453 distance: 131 - 132: 30.201 distance: 131 - 133: 9.006 distance: 134 - 135: 8.460 distance: 135 - 136: 20.094 distance: 135 - 138: 19.527 distance: 136 - 137: 9.279 distance: 136 - 145: 4.661 distance: 138 - 139: 13.555 distance: 139 - 140: 31.754 distance: 140 - 141: 15.663 distance: 141 - 142: 12.516 distance: 142 - 143: 18.053 distance: 142 - 144: 17.547 distance: 145 - 146: 6.912 distance: 146 - 147: 6.781 distance: 146 - 149: 22.319 distance: 147 - 148: 17.134 distance: 147 - 156: 17.127 distance: 149 - 150: 12.503 distance: 150 - 151: 20.141 distance: 151 - 152: 8.083 distance: 152 - 153: 7.050 distance: 153 - 154: 4.628 distance: 156 - 157: 8.696 distance: 157 - 158: 10.459 distance: 157 - 160: 19.208 distance: 158 - 159: 14.558 distance: 158 - 165: 18.439 distance: 160 - 161: 9.207 distance: 161 - 162: 3.614 distance: 162 - 163: 21.429 distance: 163 - 164: 12.985 distance: 165 - 166: 20.391 distance: 166 - 167: 18.448 distance: 166 - 169: 21.567 distance: 167 - 168: 32.536 distance: 167 - 176: 11.416 distance: 169 - 170: 19.304 distance: 170 - 171: 13.749 distance: 170 - 172: 6.083 distance: 171 - 173: 27.878 distance: 172 - 174: 14.706 distance: 173 - 175: 13.355 distance: 174 - 175: 15.451 distance: 176 - 177: 7.379 distance: 177 - 178: 20.447 distance: 177 - 180: 20.747 distance: 178 - 179: 16.652 distance: 178 - 182: 14.900 distance: 180 - 181: 44.139