Starting phenix.real_space_refine on Thu Feb 15 23:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kuv_9888/02_2024/6kuv_9888_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 116 5.16 5 C 8629 2.51 5 N 2338 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" 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 "A ARG 568": "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 578": "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 150": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13720 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5625 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 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: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5599 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 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: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 3} Chain: "V" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 285 Classifications: {'RNA': 13} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Time building chain proxies: 7.66, per 1000 atoms: 0.56 Number of scatterers: 13720 At special positions: 0 Unit cell: (110.16, 127.84, 122.4, 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 116 16.00 P 23 15.00 O 2614 8.00 N 2338 7.00 C 8629 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: 4.96 Conformation dependent library (CDL) restraints added in 2.3 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 48.5% alpha, 7.7% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.989A pdb=" N ASN A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 4.047A pdb=" N ILE A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 150 through 170 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.515A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.186A 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 296 through 300 removed outlier: 3.712A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) 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 removed outlier: 3.545A pdb=" N GLU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.703A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.584A pdb=" N ARG A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 569 through 589 removed outlier: 4.335A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 removed outlier: 3.822A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.601A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.619A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 12 " --> pdb=" O MET B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.782A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.797A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.589A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.543A 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: 3.590A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.811A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.752A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.762A 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 392 removed outlier: 3.642A pdb=" N THR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.726A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.539A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.775A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 668 through 672 removed outlier: 4.170A pdb=" N LEU B 671 " --> pdb=" O ARG B 668 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 672' Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.858A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.657A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.642A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.790A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.690A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.722A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.696A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.720A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.220A pdb=" N GLU C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.543A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU C 237 " --> pdb=" O GLU C 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.561A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 243' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.341A pdb=" N GLU A 105 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 133 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY A 107 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.555A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.358A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.538A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.502A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.601A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 567 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3745 1.33 - 1.46: 2605 1.46 - 1.58: 7448 1.58 - 1.70: 44 1.70 - 1.82: 192 Bond restraints: 14034 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.378 -0.045 8.40e-03 1.42e+04 2.84e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.76e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.12e+00 bond pdb=" N ILE B 731 " pdb=" CA ILE B 731 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N ILE B 730 " pdb=" CA ILE B 730 " ideal model delta sigma weight residual 1.459 1.431 0.028 1.25e-02 6.40e+03 5.00e+00 ... (remaining 14029 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.26: 484 106.26 - 113.23: 7386 113.23 - 120.19: 5417 120.19 - 127.16: 5502 127.16 - 134.12: 177 Bond angle restraints: 18966 Sorted by residual: angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.53 106.94 6.59 9.80e-01 1.04e+00 4.52e+01 angle pdb=" N ILE B 393 " pdb=" CA ILE B 393 " pdb=" C ILE B 393 " ideal model delta sigma weight residual 113.20 107.64 5.56 9.60e-01 1.09e+00 3.35e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.42 -4.85 1.25e+00 6.40e-01 1.51e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLN A 358 " pdb=" CB GLN A 358 " pdb=" CG GLN A 358 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 ... (remaining 18961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8531 35.86 - 71.72: 82 71.72 - 107.57: 8 107.57 - 143.43: 0 143.43 - 179.29: 4 Dihedral angle restraints: 8625 sinusoidal: 3837 harmonic: 4788 Sorted by residual: dihedral pdb=" O4' U V 5 " pdb=" C1' U V 5 " pdb=" N1 U V 5 " pdb=" C2 U V 5 " ideal model delta sinusoidal sigma weight residual 232.00 52.71 179.29 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 7 " pdb=" C1' C R 7 " pdb=" N1 C R 7 " pdb=" C2 C R 7 " ideal model delta sinusoidal sigma weight residual -128.00 51.08 -179.08 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 4 " pdb=" C1' U R 4 " pdb=" N1 U R 4 " pdb=" C2 U R 4 " ideal model delta sinusoidal sigma weight residual -128.00 48.06 -176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1660 0.058 - 0.116: 353 0.116 - 0.174: 57 0.174 - 0.232: 5 0.232 - 0.290: 4 Chirality restraints: 2079 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 2.36 0.29 2.00e-01 2.50e+01 2.10e+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 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2076 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 422 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.21e+01 pdb=" C LYS A 422 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS A 422 " 0.023 2.00e-02 2.50e+03 pdb=" N MET A 423 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 423 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C MET A 423 " 0.060 2.00e-02 2.50e+03 pdb=" O MET A 423 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS A 424 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE A 628 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.020 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1198 2.75 - 3.28: 12752 3.28 - 3.82: 20932 3.82 - 4.36: 25381 4.36 - 4.90: 43484 Nonbonded interactions: 103747 Sorted by model distance: nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.206 2.520 nonbonded pdb=" OE2 GLU A 408 " pdb=" NH2 ARG B 557 " model vdw 2.230 2.520 nonbonded pdb=" OH TYR B 320 " pdb=" OG SER B 417 " model vdw 2.287 2.440 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.289 2.440 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.293 2.440 ... (remaining 103742 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: 0.280 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: 2.090 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.870 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.003 0.058 14034 Z= 0.222 Angle : 0.793 10.221 18966 Z= 0.447 Chirality : 0.050 0.290 2079 Planarity : 0.006 0.065 2333 Dihedral : 11.910 179.287 5517 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 0.28 % Allowed : 2.28 % Favored : 97.44 % 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: -4.84 (0.15), residues: 1618 helix: -3.33 (0.12), residues: 716 sheet: -1.95 (0.45), residues: 138 loop : -3.31 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 386 HIS 0.008 0.001 HIS A 451 PHE 0.022 0.002 PHE B 420 TYR 0.017 0.002 TYR B 38 ARG 0.006 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 598 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4421 (ttp80) cc_final: 0.3887 (mtm-85) REVERT: A 43 GLN cc_start: 0.7455 (tt0) cc_final: 0.7218 (tp-100) REVERT: A 121 PHE cc_start: 0.4748 (t80) cc_final: 0.4488 (t80) REVERT: A 291 PHE cc_start: 0.7882 (m-80) cc_final: 0.6786 (m-80) REVERT: A 419 TYR cc_start: 0.7818 (t80) cc_final: 0.7532 (t80) REVERT: A 435 ASN cc_start: 0.7487 (m-40) cc_final: 0.6975 (t0) REVERT: A 457 PHE cc_start: 0.8099 (m-80) cc_final: 0.7546 (m-80) REVERT: A 492 ASN cc_start: 0.6371 (m-40) cc_final: 0.5653 (p0) REVERT: A 578 GLU cc_start: 0.7817 (tt0) cc_final: 0.7124 (tt0) REVERT: A 653 LEU cc_start: 0.8041 (mp) cc_final: 0.7715 (mp) REVERT: B 46 THR cc_start: 0.8474 (m) cc_final: 0.7942 (t) REVERT: B 90 MET cc_start: 0.8749 (ppp) cc_final: 0.8516 (ptm) REVERT: B 138 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6744 (ttm-80) REVERT: B 180 GLU cc_start: 0.6231 (tt0) cc_final: 0.5988 (mp0) REVERT: B 219 PHE cc_start: 0.8465 (t80) cc_final: 0.8028 (t80) REVERT: B 357 PHE cc_start: 0.6732 (p90) cc_final: 0.6365 (p90) REVERT: B 446 ASP cc_start: 0.8334 (p0) cc_final: 0.7588 (p0) REVERT: B 494 THR cc_start: 0.8449 (p) cc_final: 0.8130 (p) REVERT: B 547 MET cc_start: 0.7978 (tpp) cc_final: 0.7712 (tpp) REVERT: B 574 MET cc_start: 0.7858 (mmm) cc_final: 0.7160 (mmm) REVERT: B 610 GLU cc_start: 0.7169 (mp0) cc_final: 0.6591 (mp0) REVERT: C 11 TYR cc_start: 0.7078 (t80) cc_final: 0.6652 (t80) REVERT: C 55 MET cc_start: 0.8904 (mmm) cc_final: 0.8363 (tpp) REVERT: C 156 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: C 178 GLU cc_start: 0.5514 (pp20) cc_final: 0.5108 (pp20) REVERT: C 209 VAL cc_start: 0.9236 (t) cc_final: 0.9035 (t) REVERT: C 225 LEU cc_start: 0.8192 (mt) cc_final: 0.7971 (mt) outliers start: 4 outliers final: 0 residues processed: 602 average time/residue: 0.3138 time to fit residues: 256.8058 Evaluate side-chains 322 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 49 optimal weight: 0.0020 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 131 HIS A 210 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS A 638 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 147 GLN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14034 Z= 0.182 Angle : 0.604 8.523 18966 Z= 0.311 Chirality : 0.041 0.190 2079 Planarity : 0.005 0.053 2333 Dihedral : 13.143 179.145 2115 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % 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: -2.96 (0.18), residues: 1618 helix: -1.09 (0.17), residues: 748 sheet: -1.04 (0.50), residues: 131 loop : -3.12 (0.18), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 357 HIS 0.006 0.001 HIS A 451 PHE 0.014 0.001 PHE A 42 TYR 0.017 0.001 TYR B 685 ARG 0.006 0.001 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 402 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4314 (ttp80) cc_final: 0.3434 (mpp-170) REVERT: A 12 PHE cc_start: 0.6646 (p90) cc_final: 0.6385 (p90) REVERT: A 291 PHE cc_start: 0.7969 (m-80) cc_final: 0.6807 (m-80) REVERT: A 419 TYR cc_start: 0.7813 (t80) cc_final: 0.7019 (t80) REVERT: A 492 ASN cc_start: 0.6401 (m-40) cc_final: 0.5539 (p0) REVERT: A 574 MET cc_start: 0.6595 (mtm) cc_final: 0.6341 (mtm) REVERT: A 578 GLU cc_start: 0.7966 (tt0) cc_final: 0.7137 (tt0) REVERT: A 638 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8166 (t0) REVERT: A 653 LEU cc_start: 0.8274 (mp) cc_final: 0.7824 (mp) REVERT: B 17 MET cc_start: 0.6513 (mpp) cc_final: 0.5819 (mpp) REVERT: B 77 ASN cc_start: 0.7912 (p0) cc_final: 0.7039 (p0) REVERT: B 138 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6805 (ttm-80) REVERT: B 178 TRP cc_start: 0.6387 (m-10) cc_final: 0.6056 (m-10) REVERT: B 357 PHE cc_start: 0.6462 (p90) cc_final: 0.6230 (p90) REVERT: B 375 MET cc_start: 0.7741 (mtm) cc_final: 0.7460 (mtp) REVERT: B 376 LYS cc_start: 0.8334 (tttt) cc_final: 0.7954 (tptt) REVERT: B 381 LEU cc_start: 0.7829 (mp) cc_final: 0.7580 (mt) REVERT: B 382 MET cc_start: 0.7025 (mtp) cc_final: 0.6564 (mmt) REVERT: B 388 ASP cc_start: 0.8631 (m-30) cc_final: 0.8060 (m-30) REVERT: B 415 MET cc_start: 0.5233 (mpp) cc_final: 0.4776 (mpp) REVERT: B 450 LEU cc_start: 0.9051 (tp) cc_final: 0.8782 (tp) REVERT: B 528 MET cc_start: 0.8309 (mtm) cc_final: 0.8107 (ttm) REVERT: B 610 GLU cc_start: 0.7137 (mp0) cc_final: 0.6780 (mp0) REVERT: B 675 MET cc_start: 0.5644 (ppp) cc_final: 0.4823 (ppp) REVERT: C 5 LEU cc_start: 0.6792 (pt) cc_final: 0.6495 (pt) REVERT: C 9 LYS cc_start: 0.7758 (mttt) cc_final: 0.7444 (ptpt) REVERT: C 156 PRO cc_start: 0.8127 (Cg_exo) cc_final: 0.7866 (Cg_endo) REVERT: C 162 ASN cc_start: 0.6585 (p0) cc_final: 0.6329 (p0) REVERT: C 163 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6778 (tm-30) REVERT: C 225 LEU cc_start: 0.8537 (mt) cc_final: 0.8194 (mt) outliers start: 2 outliers final: 0 residues processed: 403 average time/residue: 0.2704 time to fit residues: 158.2388 Evaluate side-chains 295 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 263 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 606 HIS A 647 ASN ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14034 Z= 0.231 Angle : 0.624 8.274 18966 Z= 0.321 Chirality : 0.042 0.197 2079 Planarity : 0.004 0.046 2333 Dihedral : 13.021 177.502 2115 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.79 % Favored : 92.15 % Rotamer: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % 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: -2.07 (0.20), residues: 1618 helix: -0.04 (0.18), residues: 748 sheet: -0.97 (0.48), residues: 141 loop : -2.99 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 386 HIS 0.006 0.001 HIS A 606 PHE 0.014 0.002 PHE A 645 TYR 0.020 0.001 TYR C 11 ARG 0.004 0.001 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 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: A 6 ARG cc_start: 0.4622 (ttp80) cc_final: 0.3658 (mpp-170) REVERT: A 291 PHE cc_start: 0.8202 (m-80) cc_final: 0.7227 (m-10) REVERT: A 413 LYS cc_start: 0.7649 (tppp) cc_final: 0.7266 (tppt) REVERT: A 419 TYR cc_start: 0.7601 (t80) cc_final: 0.7373 (t80) REVERT: A 457 PHE cc_start: 0.8110 (m-80) cc_final: 0.7895 (m-80) REVERT: A 492 ASN cc_start: 0.6615 (m-40) cc_final: 0.6017 (p0) REVERT: A 578 GLU cc_start: 0.8068 (tt0) cc_final: 0.7341 (mt-10) REVERT: A 649 GLN cc_start: 0.8519 (pt0) cc_final: 0.8227 (pt0) REVERT: A 653 LEU cc_start: 0.8417 (mp) cc_final: 0.8074 (mp) REVERT: B 77 ASN cc_start: 0.8571 (p0) cc_final: 0.7981 (p0) REVERT: B 101 MET cc_start: 0.6951 (pmm) cc_final: 0.6686 (pmm) REVERT: B 138 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.6719 (ttm-80) REVERT: B 157 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7671 (pp30) REVERT: B 166 VAL cc_start: 0.7869 (m) cc_final: 0.7285 (m) REVERT: B 178 TRP cc_start: 0.6825 (m-10) cc_final: 0.6381 (m-10) REVERT: B 258 GLU cc_start: 0.6885 (tp30) cc_final: 0.6271 (mm-30) REVERT: B 310 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7396 (mmmt) REVERT: B 323 MET cc_start: 0.7197 (tpp) cc_final: 0.6908 (tpp) REVERT: B 357 PHE cc_start: 0.6485 (p90) cc_final: 0.6089 (p90) REVERT: B 375 MET cc_start: 0.7933 (mtm) cc_final: 0.7485 (mtp) REVERT: B 376 LYS cc_start: 0.8251 (tttt) cc_final: 0.7997 (tptm) REVERT: B 381 LEU cc_start: 0.7923 (mp) cc_final: 0.7405 (mt) REVERT: B 382 MET cc_start: 0.7238 (mtp) cc_final: 0.7017 (mmt) REVERT: B 391 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7097 (pt0) REVERT: B 415 MET cc_start: 0.5464 (mpp) cc_final: 0.4544 (mtm) REVERT: B 423 MET cc_start: 0.7982 (mtp) cc_final: 0.7645 (mtm) REVERT: B 427 TYR cc_start: 0.8385 (t80) cc_final: 0.8093 (t80) REVERT: B 523 ASP cc_start: 0.7569 (m-30) cc_final: 0.7150 (m-30) REVERT: B 594 ASP cc_start: 0.8632 (m-30) cc_final: 0.8301 (m-30) REVERT: B 604 SER cc_start: 0.8879 (m) cc_final: 0.7799 (t) REVERT: B 675 MET cc_start: 0.6233 (ppp) cc_final: 0.5944 (ppp) REVERT: B 678 MET cc_start: 0.5755 (mpp) cc_final: 0.5218 (tmm) REVERT: C 5 LEU cc_start: 0.7096 (pt) cc_final: 0.6817 (pt) REVERT: C 9 LYS cc_start: 0.8228 (mttt) cc_final: 0.7680 (ptpt) REVERT: C 162 ASN cc_start: 0.6722 (p0) cc_final: 0.6358 (p0) REVERT: C 225 LEU cc_start: 0.8480 (mt) cc_final: 0.8223 (mt) REVERT: C 236 MET cc_start: 0.8010 (mmp) cc_final: 0.7764 (mmp) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.2693 time to fit residues: 142.7049 Evaluate side-chains 280 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 638 ASN B 84 ASN B 316 GLN B 348 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 106 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14034 Z= 0.188 Angle : 0.585 7.837 18966 Z= 0.299 Chirality : 0.041 0.213 2079 Planarity : 0.004 0.043 2333 Dihedral : 12.975 179.480 2115 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % 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: -1.57 (0.20), residues: 1618 helix: 0.47 (0.19), residues: 753 sheet: -0.91 (0.48), residues: 141 loop : -2.83 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.022 0.001 PHE B 219 TYR 0.017 0.001 TYR C 11 ARG 0.004 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 1.498 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: A 6 ARG cc_start: 0.4584 (ttp80) cc_final: 0.3641 (mpp-170) REVERT: A 128 MET cc_start: 0.6800 (mpp) cc_final: 0.6133 (mpp) REVERT: A 291 PHE cc_start: 0.8129 (m-80) cc_final: 0.7141 (m-10) REVERT: A 353 GLN cc_start: 0.5765 (tm-30) cc_final: 0.5482 (tm-30) REVERT: A 419 TYR cc_start: 0.7532 (t80) cc_final: 0.7151 (t80) REVERT: A 423 MET cc_start: 0.7864 (mtt) cc_final: 0.7138 (mtt) REVERT: A 492 ASN cc_start: 0.6864 (m-40) cc_final: 0.5943 (p0) REVERT: A 555 MET cc_start: 0.8084 (mmm) cc_final: 0.7782 (mmm) REVERT: A 578 GLU cc_start: 0.8111 (tt0) cc_final: 0.7533 (mt-10) REVERT: A 680 CYS cc_start: 0.8275 (t) cc_final: 0.7571 (t) REVERT: B 77 ASN cc_start: 0.8627 (p0) cc_final: 0.8134 (p0) REVERT: B 85 VAL cc_start: 0.8501 (t) cc_final: 0.8296 (t) REVERT: B 101 MET cc_start: 0.7385 (pmm) cc_final: 0.6881 (pmm) REVERT: B 138 ARG cc_start: 0.7272 (mtp-110) cc_final: 0.6551 (ttm-80) REVERT: B 157 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7499 (pp30) REVERT: B 166 VAL cc_start: 0.8084 (m) cc_final: 0.7466 (m) REVERT: B 178 TRP cc_start: 0.6927 (m-10) cc_final: 0.6488 (m-10) REVERT: B 310 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7441 (mmmt) REVERT: B 357 PHE cc_start: 0.6618 (p90) cc_final: 0.6301 (p90) REVERT: B 375 MET cc_start: 0.7881 (mtm) cc_final: 0.7357 (mtp) REVERT: B 376 LYS cc_start: 0.8290 (tttt) cc_final: 0.8060 (tptm) REVERT: B 381 LEU cc_start: 0.7978 (mp) cc_final: 0.7438 (mt) REVERT: B 382 MET cc_start: 0.7291 (mtp) cc_final: 0.6717 (mmt) REVERT: B 465 LEU cc_start: 0.9039 (mm) cc_final: 0.8447 (mm) REVERT: B 523 ASP cc_start: 0.7409 (m-30) cc_final: 0.7062 (m-30) REVERT: B 594 ASP cc_start: 0.8654 (m-30) cc_final: 0.8301 (m-30) REVERT: B 604 SER cc_start: 0.8836 (m) cc_final: 0.7900 (t) REVERT: B 675 MET cc_start: 0.6342 (ppp) cc_final: 0.5988 (ppp) REVERT: B 678 MET cc_start: 0.5679 (mpp) cc_final: 0.5087 (tmm) REVERT: B 682 GLU cc_start: 0.8495 (tt0) cc_final: 0.7759 (tm-30) REVERT: B 686 GLN cc_start: 0.7196 (mm110) cc_final: 0.6614 (mm-40) REVERT: C 5 LEU cc_start: 0.6955 (pt) cc_final: 0.6646 (pt) REVERT: C 6 THR cc_start: 0.7173 (p) cc_final: 0.6368 (p) REVERT: C 9 LYS cc_start: 0.8263 (mttt) cc_final: 0.7653 (ptpt) REVERT: C 162 ASN cc_start: 0.6879 (p0) cc_final: 0.6512 (p0) REVERT: C 186 ILE cc_start: 0.4895 (mp) cc_final: 0.4682 (mm) REVERT: C 225 LEU cc_start: 0.8474 (mt) cc_final: 0.8238 (mt) REVERT: C 234 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 236 MET cc_start: 0.8021 (mmp) cc_final: 0.7684 (mmp) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.2591 time to fit residues: 134.3979 Evaluate side-chains 272 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN B 316 GLN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14034 Z= 0.193 Angle : 0.590 8.198 18966 Z= 0.300 Chirality : 0.041 0.213 2079 Planarity : 0.004 0.043 2333 Dihedral : 12.990 179.349 2115 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.07 % 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: -1.46 (0.21), residues: 1618 helix: 0.58 (0.19), residues: 758 sheet: -1.09 (0.47), residues: 142 loop : -2.76 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 357 HIS 0.004 0.001 HIS A 242 PHE 0.017 0.001 PHE B 219 TYR 0.013 0.001 TYR B 560 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4498 (ttp80) cc_final: 0.3641 (mpp-170) REVERT: A 128 MET cc_start: 0.6739 (mpp) cc_final: 0.6005 (mpp) REVERT: A 212 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6453 (ttm170) REVERT: A 291 PHE cc_start: 0.8111 (m-80) cc_final: 0.6970 (m-10) REVERT: A 354 GLU cc_start: 0.6012 (tp30) cc_final: 0.5543 (tm-30) REVERT: A 423 MET cc_start: 0.7724 (mtt) cc_final: 0.7046 (mtt) REVERT: A 457 PHE cc_start: 0.7953 (m-80) cc_final: 0.7741 (m-80) REVERT: A 555 MET cc_start: 0.8082 (mmm) cc_final: 0.7738 (mmm) REVERT: A 578 GLU cc_start: 0.8139 (tt0) cc_final: 0.7672 (mt-10) REVERT: A 680 CYS cc_start: 0.8324 (t) cc_final: 0.7569 (t) REVERT: B 77 ASN cc_start: 0.8621 (p0) cc_final: 0.7990 (p0) REVERT: B 101 MET cc_start: 0.7281 (pmm) cc_final: 0.6722 (pmm) REVERT: B 138 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6547 (ttm-80) REVERT: B 157 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7511 (pp30) REVERT: B 178 TRP cc_start: 0.6866 (m-10) cc_final: 0.6421 (m-10) REVERT: B 310 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7362 (mmmt) REVERT: B 357 PHE cc_start: 0.6630 (p90) cc_final: 0.6370 (p90) REVERT: B 375 MET cc_start: 0.7926 (mtm) cc_final: 0.7389 (mtp) REVERT: B 381 LEU cc_start: 0.8051 (mp) cc_final: 0.7537 (mt) REVERT: B 391 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7317 (mp0) REVERT: B 443 GLN cc_start: 0.9096 (tp40) cc_final: 0.8436 (tp40) REVERT: B 523 ASP cc_start: 0.7559 (m-30) cc_final: 0.7130 (m-30) REVERT: B 594 ASP cc_start: 0.8577 (m-30) cc_final: 0.8188 (m-30) REVERT: B 604 SER cc_start: 0.8870 (m) cc_final: 0.8002 (t) REVERT: B 611 ILE cc_start: 0.9001 (mt) cc_final: 0.8684 (mt) REVERT: B 675 MET cc_start: 0.6396 (ppp) cc_final: 0.5869 (ppp) REVERT: B 682 GLU cc_start: 0.8688 (tt0) cc_final: 0.7983 (tm-30) REVERT: B 686 GLN cc_start: 0.6969 (mm110) cc_final: 0.6522 (mm-40) REVERT: C 225 LEU cc_start: 0.8400 (mt) cc_final: 0.8144 (mt) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.2459 time to fit residues: 126.3297 Evaluate side-chains 272 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 39 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN B 316 GLN B 348 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN C 106 ASN C 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14034 Z= 0.152 Angle : 0.565 8.524 18966 Z= 0.288 Chirality : 0.041 0.217 2079 Planarity : 0.003 0.044 2333 Dihedral : 12.952 179.553 2115 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % 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: -1.29 (0.21), residues: 1618 helix: 0.74 (0.19), residues: 757 sheet: -1.13 (0.46), residues: 143 loop : -2.65 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 357 HIS 0.004 0.001 HIS A 242 PHE 0.020 0.001 PHE A 341 TYR 0.014 0.001 TYR B 560 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.4438 (ttp80) cc_final: 0.3569 (mtm-85) REVERT: A 43 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7421 (mm-40) REVERT: A 128 MET cc_start: 0.6678 (mpp) cc_final: 0.6310 (mpp) REVERT: A 212 ARG cc_start: 0.7717 (ttm170) cc_final: 0.6779 (ttm170) REVERT: A 291 PHE cc_start: 0.8017 (m-80) cc_final: 0.7014 (m-10) REVERT: A 354 GLU cc_start: 0.6104 (tp30) cc_final: 0.5873 (tm-30) REVERT: A 578 GLU cc_start: 0.8358 (tt0) cc_final: 0.7895 (mt-10) REVERT: A 671 LYS cc_start: 0.7892 (tptm) cc_final: 0.7402 (tptm) REVERT: A 675 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 77 ASN cc_start: 0.8534 (p0) cc_final: 0.8143 (p0) REVERT: B 101 MET cc_start: 0.7296 (pmm) cc_final: 0.6617 (pmm) REVERT: B 138 ARG cc_start: 0.7113 (mtp-110) cc_final: 0.6379 (ttm-80) REVERT: B 165 MET cc_start: 0.7475 (mtp) cc_final: 0.7224 (mtp) REVERT: B 176 MET cc_start: 0.6483 (mtm) cc_final: 0.6146 (mtm) REVERT: B 178 TRP cc_start: 0.6876 (m-10) cc_final: 0.6304 (m-10) REVERT: B 310 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7436 (mmmt) REVERT: B 357 PHE cc_start: 0.6626 (p90) cc_final: 0.6084 (p90) REVERT: B 375 MET cc_start: 0.7938 (mtm) cc_final: 0.7316 (mtp) REVERT: B 376 LYS cc_start: 0.8413 (tttt) cc_final: 0.8160 (tptm) REVERT: B 391 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7348 (pt0) REVERT: B 415 MET cc_start: 0.5431 (mpp) cc_final: 0.5024 (mpp) REVERT: B 443 GLN cc_start: 0.9034 (tp40) cc_final: 0.8363 (tp40) REVERT: B 523 ASP cc_start: 0.7568 (m-30) cc_final: 0.7262 (m-30) REVERT: B 547 MET cc_start: 0.7499 (tpp) cc_final: 0.7254 (mtt) REVERT: B 594 ASP cc_start: 0.8536 (m-30) cc_final: 0.8144 (m-30) REVERT: B 604 SER cc_start: 0.8972 (m) cc_final: 0.8011 (t) REVERT: B 675 MET cc_start: 0.7035 (ppp) cc_final: 0.6700 (ppp) REVERT: B 681 GLU cc_start: 0.8352 (pp20) cc_final: 0.7701 (pp20) REVERT: B 682 GLU cc_start: 0.8977 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 686 GLN cc_start: 0.6929 (mm110) cc_final: 0.6548 (mm-40) REVERT: C 5 LEU cc_start: 0.7425 (pt) cc_final: 0.7083 (pt) REVERT: C 9 LYS cc_start: 0.7893 (mttm) cc_final: 0.7526 (ptpp) REVERT: C 163 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 225 LEU cc_start: 0.8308 (mt) cc_final: 0.8065 (mt) REVERT: C 234 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7685 (mm-30) REVERT: C 236 MET cc_start: 0.8440 (mmp) cc_final: 0.8185 (mmp) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.2500 time to fit residues: 128.3254 Evaluate side-chains 270 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 316 GLN B 348 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14034 Z= 0.207 Angle : 0.610 8.534 18966 Z= 0.310 Chirality : 0.042 0.215 2079 Planarity : 0.004 0.049 2333 Dihedral : 12.984 178.513 2115 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 0.07 % Allowed : 1.04 % Favored : 98.90 % 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: -1.32 (0.20), residues: 1618 helix: 0.66 (0.19), residues: 757 sheet: -1.14 (0.45), residues: 141 loop : -2.61 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 357 HIS 0.005 0.001 HIS B 660 PHE 0.018 0.001 PHE A 292 TYR 0.012 0.001 TYR B 560 ARG 0.005 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.5317 (mtt180) cc_final: 0.4903 (tpp-160) REVERT: A 43 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7539 (mm110) REVERT: A 128 MET cc_start: 0.6533 (mpp) cc_final: 0.5931 (mpp) REVERT: A 212 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7297 (ttm170) REVERT: A 291 PHE cc_start: 0.8065 (m-80) cc_final: 0.6914 (m-10) REVERT: A 354 GLU cc_start: 0.6029 (tp30) cc_final: 0.5266 (mt-10) REVERT: A 578 GLU cc_start: 0.8463 (tt0) cc_final: 0.8008 (mt-10) REVERT: A 693 ARG cc_start: 0.8712 (mpt180) cc_final: 0.7908 (tpt170) REVERT: B 4 ASN cc_start: 0.8342 (t0) cc_final: 0.7714 (t0) REVERT: B 77 ASN cc_start: 0.8573 (p0) cc_final: 0.8136 (p0) REVERT: B 85 VAL cc_start: 0.8498 (t) cc_final: 0.8288 (t) REVERT: B 101 MET cc_start: 0.7406 (pmm) cc_final: 0.6604 (pmm) REVERT: B 138 ARG cc_start: 0.7392 (mtp-110) cc_final: 0.6528 (ttm-80) REVERT: B 157 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7387 (pp30) REVERT: B 165 MET cc_start: 0.7476 (mtp) cc_final: 0.7220 (mtp) REVERT: B 176 MET cc_start: 0.6574 (mtm) cc_final: 0.6263 (mtm) REVERT: B 178 TRP cc_start: 0.6952 (m-10) cc_final: 0.6639 (m-10) REVERT: B 357 PHE cc_start: 0.6718 (p90) cc_final: 0.6351 (p90) REVERT: B 375 MET cc_start: 0.8025 (mtm) cc_final: 0.7213 (mtp) REVERT: B 376 LYS cc_start: 0.8453 (tttt) cc_final: 0.8093 (tptm) REVERT: B 391 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7425 (pt0) REVERT: B 415 MET cc_start: 0.5416 (mpp) cc_final: 0.4963 (mtm) REVERT: B 443 GLN cc_start: 0.9129 (tp40) cc_final: 0.8454 (tp40) REVERT: B 481 GLU cc_start: 0.7295 (mp0) cc_final: 0.7011 (pm20) REVERT: B 523 ASP cc_start: 0.7410 (m-30) cc_final: 0.7084 (m-30) REVERT: B 555 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 594 ASP cc_start: 0.8642 (m-30) cc_final: 0.8217 (m-30) REVERT: B 604 SER cc_start: 0.9112 (m) cc_final: 0.8088 (t) REVERT: B 675 MET cc_start: 0.7025 (ppp) cc_final: 0.6820 (ppp) REVERT: B 682 GLU cc_start: 0.8955 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 686 GLN cc_start: 0.7161 (mm110) cc_final: 0.6672 (mm-40) REVERT: C 6 THR cc_start: 0.7382 (p) cc_final: 0.6961 (p) REVERT: C 9 LYS cc_start: 0.7856 (mttm) cc_final: 0.7502 (ptpp) REVERT: C 10 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 225 LEU cc_start: 0.8176 (mt) cc_final: 0.7970 (mt) REVERT: C 234 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 236 MET cc_start: 0.8664 (mmp) cc_final: 0.8096 (mmt) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.2519 time to fit residues: 124.4181 Evaluate side-chains 264 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN B 348 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 600 ASN C 106 ASN C 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14034 Z= 0.201 Angle : 0.610 8.818 18966 Z= 0.311 Chirality : 0.042 0.222 2079 Planarity : 0.004 0.051 2333 Dihedral : 13.015 178.736 2115 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.03 % Rotamer: Outliers : 0.07 % Allowed : 1.10 % 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: -1.30 (0.21), residues: 1618 helix: 0.70 (0.19), residues: 761 sheet: -1.32 (0.46), residues: 133 loop : -2.60 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 357 HIS 0.004 0.001 HIS B 660 PHE 0.014 0.001 PHE A 652 TYR 0.013 0.001 TYR C 11 ARG 0.005 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7484 (mm110) REVERT: A 128 MET cc_start: 0.6535 (mpp) cc_final: 0.5927 (mpp) REVERT: A 212 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7124 (ttm170) REVERT: A 291 PHE cc_start: 0.8118 (m-80) cc_final: 0.6960 (m-10) REVERT: A 578 GLU cc_start: 0.8430 (tt0) cc_final: 0.8061 (mt-10) REVERT: A 598 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 693 ARG cc_start: 0.8749 (mpt180) cc_final: 0.7930 (tpt170) REVERT: B 4 ASN cc_start: 0.8450 (t0) cc_final: 0.7303 (t0) REVERT: B 77 ASN cc_start: 0.8579 (p0) cc_final: 0.8137 (p0) REVERT: B 101 MET cc_start: 0.7367 (pmm) cc_final: 0.6558 (pmm) REVERT: B 138 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6487 (ttm-80) REVERT: B 161 LYS cc_start: 0.7719 (mppt) cc_final: 0.7479 (mmtm) REVERT: B 176 MET cc_start: 0.6469 (mtm) cc_final: 0.6089 (mtm) REVERT: B 178 TRP cc_start: 0.6987 (m-10) cc_final: 0.6711 (m-10) REVERT: B 357 PHE cc_start: 0.6778 (p90) cc_final: 0.6437 (p90) REVERT: B 375 MET cc_start: 0.8105 (mtm) cc_final: 0.7289 (mtp) REVERT: B 376 LYS cc_start: 0.8408 (tttt) cc_final: 0.8029 (tptm) REVERT: B 391 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7456 (pt0) REVERT: B 467 PHE cc_start: 0.9463 (t80) cc_final: 0.9130 (t80) REVERT: B 481 GLU cc_start: 0.7499 (mp0) cc_final: 0.7154 (pm20) REVERT: B 523 ASP cc_start: 0.7522 (m-30) cc_final: 0.7255 (m-30) REVERT: B 555 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7112 (mm-30) REVERT: B 594 ASP cc_start: 0.8654 (m-30) cc_final: 0.8279 (m-30) REVERT: B 604 SER cc_start: 0.9128 (m) cc_final: 0.8096 (t) REVERT: B 675 MET cc_start: 0.6921 (ppp) cc_final: 0.6581 (ppp) REVERT: B 691 MET cc_start: 0.8171 (tpp) cc_final: 0.7759 (mtt) REVERT: B 710 MET cc_start: 0.6784 (tpp) cc_final: 0.6463 (tpp) REVERT: C 6 THR cc_start: 0.7236 (p) cc_final: 0.6888 (p) REVERT: C 9 LYS cc_start: 0.7781 (mttm) cc_final: 0.7487 (ptpp) REVERT: C 94 MET cc_start: 0.6726 (tpp) cc_final: 0.6303 (tpp) REVERT: C 163 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 225 LEU cc_start: 0.8206 (mt) cc_final: 0.7969 (mt) REVERT: C 234 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7754 (mm-30) REVERT: C 236 MET cc_start: 0.8808 (mmp) cc_final: 0.8215 (mmt) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.2401 time to fit residues: 118.4133 Evaluate side-chains 261 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 GLN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14034 Z= 0.172 Angle : 0.616 10.424 18966 Z= 0.309 Chirality : 0.041 0.216 2079 Planarity : 0.004 0.049 2333 Dihedral : 13.010 179.953 2115 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.20 (0.21), residues: 1618 helix: 0.83 (0.19), residues: 753 sheet: -1.30 (0.46), residues: 130 loop : -2.56 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 38 HIS 0.002 0.001 HIS A 451 PHE 0.012 0.001 PHE A 158 TYR 0.015 0.001 TYR B 560 ARG 0.009 0.000 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.5270 (mtt180) cc_final: 0.4916 (tpp-160) REVERT: A 43 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7316 (mm110) REVERT: A 128 MET cc_start: 0.6524 (mpp) cc_final: 0.6216 (mpp) REVERT: A 291 PHE cc_start: 0.7992 (m-80) cc_final: 0.6884 (m-10) REVERT: A 409 MET cc_start: 0.6846 (mmt) cc_final: 0.6336 (ttp) REVERT: A 578 GLU cc_start: 0.8409 (tt0) cc_final: 0.8023 (mt-10) REVERT: A 590 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 598 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6685 (mm-30) REVERT: A 632 PHE cc_start: 0.9216 (t80) cc_final: 0.8882 (t80) REVERT: A 675 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 693 ARG cc_start: 0.8667 (mpt180) cc_final: 0.7871 (tpt170) REVERT: B 4 ASN cc_start: 0.8362 (t0) cc_final: 0.7671 (t0) REVERT: B 77 ASN cc_start: 0.8527 (p0) cc_final: 0.8124 (p0) REVERT: B 101 MET cc_start: 0.7523 (pmm) cc_final: 0.6566 (pmm) REVERT: B 138 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.6451 (ttm-80) REVERT: B 176 MET cc_start: 0.6365 (mtm) cc_final: 0.6037 (mtm) REVERT: B 178 TRP cc_start: 0.6915 (m-10) cc_final: 0.6561 (m-10) REVERT: B 357 PHE cc_start: 0.6574 (p90) cc_final: 0.6213 (p90) REVERT: B 375 MET cc_start: 0.8055 (mtm) cc_final: 0.7245 (mtp) REVERT: B 376 LYS cc_start: 0.8402 (tttt) cc_final: 0.8032 (tptm) REVERT: B 391 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7464 (pt0) REVERT: B 446 ASP cc_start: 0.7747 (p0) cc_final: 0.7009 (t70) REVERT: B 523 ASP cc_start: 0.7448 (m-30) cc_final: 0.7101 (m-30) REVERT: B 594 ASP cc_start: 0.8645 (m-30) cc_final: 0.8228 (m-30) REVERT: B 604 SER cc_start: 0.9137 (m) cc_final: 0.8122 (t) REVERT: B 675 MET cc_start: 0.7587 (ppp) cc_final: 0.6652 (ppp) REVERT: B 678 MET cc_start: 0.4609 (tmm) cc_final: 0.4003 (tmm) REVERT: B 691 MET cc_start: 0.8156 (tpp) cc_final: 0.7945 (mtt) REVERT: B 710 MET cc_start: 0.6658 (tpp) cc_final: 0.6282 (tpp) REVERT: C 234 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 236 MET cc_start: 0.8853 (mmp) cc_final: 0.8225 (mmt) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2355 time to fit residues: 117.1953 Evaluate side-chains 265 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 130 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 638 ASN B 296 GLN B 312 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN C 106 ASN C 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14034 Z= 0.193 Angle : 0.639 10.395 18966 Z= 0.321 Chirality : 0.043 0.280 2079 Planarity : 0.004 0.053 2333 Dihedral : 12.993 178.120 2115 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.59 % 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: -1.19 (0.21), residues: 1618 helix: 0.83 (0.19), residues: 746 sheet: -1.18 (0.46), residues: 133 loop : -2.53 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.017 0.001 PHE A 42 TYR 0.014 0.001 TYR C 104 ARG 0.010 0.001 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 325 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.5666 (mtt180) cc_final: 0.5119 (tpp-160) REVERT: A 43 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7348 (mm110) REVERT: A 128 MET cc_start: 0.6413 (mpp) cc_final: 0.6069 (mpp) REVERT: A 291 PHE cc_start: 0.8023 (m-80) cc_final: 0.6868 (m-10) REVERT: A 409 MET cc_start: 0.6775 (mmt) cc_final: 0.6324 (ttp) REVERT: A 423 MET cc_start: 0.7889 (mtt) cc_final: 0.7495 (mtt) REVERT: A 578 GLU cc_start: 0.8396 (tt0) cc_final: 0.8072 (mt-10) REVERT: A 590 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 598 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 77 ASN cc_start: 0.8569 (p0) cc_final: 0.8110 (p0) REVERT: B 101 MET cc_start: 0.7534 (pmm) cc_final: 0.6516 (pmm) REVERT: B 138 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6300 (ttm-80) REVERT: B 178 TRP cc_start: 0.6946 (m-10) cc_final: 0.6642 (m-10) REVERT: B 375 MET cc_start: 0.8155 (mtm) cc_final: 0.7302 (mtp) REVERT: B 376 LYS cc_start: 0.8408 (tttt) cc_final: 0.8024 (tptm) REVERT: B 391 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7627 (pt0) REVERT: B 436 ASN cc_start: 0.7666 (m-40) cc_final: 0.7356 (m-40) REVERT: B 446 ASP cc_start: 0.7858 (p0) cc_final: 0.7101 (t70) REVERT: B 519 ASN cc_start: 0.6624 (m110) cc_final: 0.5655 (m110) REVERT: B 523 ASP cc_start: 0.7340 (m-30) cc_final: 0.7033 (m-30) REVERT: B 594 ASP cc_start: 0.8758 (m-30) cc_final: 0.8406 (m-30) REVERT: B 675 MET cc_start: 0.7589 (ppp) cc_final: 0.6878 (ppp) REVERT: B 678 MET cc_start: 0.4607 (tmm) cc_final: 0.4192 (tmm) REVERT: B 710 MET cc_start: 0.6658 (tpp) cc_final: 0.6297 (tpp) REVERT: C 234 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 236 MET cc_start: 0.8956 (mmp) cc_final: 0.8352 (mmt) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.2428 time to fit residues: 116.8958 Evaluate side-chains 257 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.0050 chunk 39 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 54 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.158225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131747 restraints weight = 23227.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134108 restraints weight = 15650.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135759 restraints weight = 11747.670| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14034 Z= 0.160 Angle : 0.614 10.213 18966 Z= 0.307 Chirality : 0.042 0.209 2079 Planarity : 0.004 0.050 2333 Dihedral : 12.966 179.930 2115 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.04 (0.21), residues: 1618 helix: 0.95 (0.19), residues: 746 sheet: -1.23 (0.45), residues: 143 loop : -2.43 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.011 0.001 PHE B 502 TYR 0.015 0.001 TYR B 560 ARG 0.008 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.02 seconds wall clock time: 58 minutes 41.86 seconds (3521.86 seconds total)