Starting phenix.real_space_refine on Sat Mar 16 07:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kut_9580/03_2024/6kut_9580_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kut_9580/03_2024/6kut_9580.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/6kut_9580/03_2024/6kut_9580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kut_9580/03_2024/6kut_9580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kut_9580/03_2024/6kut_9580_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kut_9580/03_2024/6kut_9580_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= 0.001 sd= 0.011 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 27 5.49 5 S 116 5.16 5 C 8862 2.51 5 N 2411 2.21 5 O 2695 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 "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" 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 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" Residue "C ARG 725": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14111 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5639 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 663} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5533 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 669} Chain breaks: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2360 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 9} 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: 8.63, per 1000 atoms: 0.61 Number of scatterers: 14111 At special positions: 0 Unit cell: (115.6, 110.16, 126.48, 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 27 15.00 O 2695 8.00 N 2411 7.00 C 8862 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: 5.22 Conformation dependent library (CDL) restraints added in 2.4 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 45.9% alpha, 7.7% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.520A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.919A pdb=" N SER A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.168A pdb=" N THR A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.701A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.501A pdb=" N ALA A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.886A 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 342 Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.870A 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: 3.663A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.811A pdb=" N THR A 573 " --> pdb=" O CYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.657A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 684 through 703 removed outlier: 3.607A pdb=" N SER A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 4.011A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.557A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.994A 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 116 removed outlier: 3.618A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 removed outlier: 3.558A pdb=" N GLN B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.637A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.518A 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 293 removed outlier: 3.579A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.845A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.646A 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: 3.618A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.800A 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: 3.868A 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 425 removed outlier: 3.596A 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 513 removed outlier: 3.789A pdb=" N ALA B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.512A pdb=" N ALA B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.617A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.900A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.570A pdb=" N GLY B 595 " --> pdb=" O ILE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.783A 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 removed outlier: 3.502A pdb=" N PHE B 626 " --> pdb=" O ARG B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 696 removed outlier: 3.611A pdb=" N LYS B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 4.473A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.646A pdb=" N TYR B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 752 " --> pdb=" O ARG B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.660A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.529A pdb=" N ILE C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.927A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 218 removed outlier: 3.806A pdb=" N PHE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.892A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 727 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: 5.854A pdb=" N GLU A 105 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 133 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.421A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.382A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.916A 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 602 through 604 Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.575A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.750A 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 Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.734A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.622A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AB6, first strand: chain 'C' and resid 736 through 740 566 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 5.71 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: 4212 1.34 - 1.46: 2632 1.46 - 1.58: 7354 1.58 - 1.70: 52 1.70 - 1.82: 191 Bond restraints: 14441 Sorted by residual: bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.27e-02 6.20e+03 9.97e+00 bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C ILE C 73 " pdb=" N PRO C 74 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.30e-02 5.92e+03 3.85e+00 bond pdb=" C LEU B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.378 -0.045 2.34e-02 1.83e+03 3.62e+00 bond pdb=" O5' C R 4 " pdb=" C5' C R 4 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.62e+00 ... (remaining 14436 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.81: 563 106.81 - 113.88: 7965 113.88 - 120.94: 6725 120.94 - 128.01: 4149 128.01 - 135.08: 131 Bond angle restraints: 19533 Sorted by residual: angle pdb=" C4' U R 9 " pdb=" C3' U R 9 " pdb=" O3' U R 9 " ideal model delta sigma weight residual 109.40 121.40 -12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.53 107.10 6.43 9.80e-01 1.04e+00 4.30e+01 angle pdb=" CA ILE C 186 " pdb=" CB ILE C 186 " pdb=" CG2 ILE C 186 " ideal model delta sigma weight residual 110.50 117.45 -6.95 1.70e+00 3.46e-01 1.67e+01 angle pdb=" CA LYS A 488 " pdb=" CB LYS A 488 " pdb=" CG LYS A 488 " ideal model delta sigma weight residual 114.10 122.18 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N ASP C 716 " pdb=" CA ASP C 716 " pdb=" C ASP C 716 " ideal model delta sigma weight residual 112.35 117.63 -5.28 1.34e+00 5.57e-01 1.55e+01 ... (remaining 19528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8763 35.93 - 71.87: 105 71.87 - 107.80: 10 107.80 - 143.73: 1 143.73 - 179.66: 1 Dihedral angle restraints: 8880 sinusoidal: 3986 harmonic: 4894 Sorted by residual: dihedral pdb=" CA LEU C 181 " pdb=" C LEU C 181 " pdb=" N ALA C 182 " pdb=" CA ALA C 182 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL C 740 " pdb=" C VAL C 740 " pdb=" N GLY C 741 " pdb=" CA GLY C 741 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE B 726 " pdb=" C PHE B 726 " pdb=" N GLU B 727 " pdb=" CA GLU B 727 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2084 0.121 - 0.242: 51 0.242 - 0.362: 5 0.362 - 0.483: 1 0.483 - 0.604: 1 Chirality restraints: 2142 Sorted by residual: chirality pdb=" C3' U R 9 " pdb=" C4' U R 9 " pdb=" O3' U R 9 " pdb=" C2' U R 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CB ILE C 186 " pdb=" CA ILE C 186 " pdb=" CG1 ILE C 186 " pdb=" CG2 ILE C 186 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.68e+00 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 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2139 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 36 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ILE A 36 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 36 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 37 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 35 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C MET A 35 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 35 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 37 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C SER A 37 " 0.048 2.00e-02 2.50e+03 pdb=" O SER A 37 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 38 " -0.016 2.00e-02 2.50e+03 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 841 2.73 - 3.27: 13142 3.27 - 3.82: 21297 3.82 - 4.36: 26311 4.36 - 4.90: 44451 Nonbonded interactions: 106042 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.191 2.520 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.248 2.520 nonbonded pdb=" O THR B 287 " pdb=" OG1 THR B 291 " model vdw 2.270 2.440 nonbonded pdb=" OG SER A 163 " pdb=" NH1 ARG A 167 " model vdw 2.282 2.520 nonbonded pdb=" O GLU C 188 " pdb=" OG SER C 191 " model vdw 2.291 2.440 ... (remaining 106037 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: 0.250 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: 2.070 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 41.590 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.052 14441 Z= 0.220 Angle : 0.807 11.996 19533 Z= 0.445 Chirality : 0.053 0.604 2142 Planarity : 0.006 0.056 2391 Dihedral : 11.953 179.664 5704 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 0.68 % Allowed : 2.17 % Favored : 97.16 % 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: -5.00 (0.15), residues: 1653 helix: -3.60 (0.11), residues: 711 sheet: -1.73 (0.42), residues: 143 loop : -3.35 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 386 HIS 0.010 0.001 HIS A 451 PHE 0.023 0.002 PHE A 156 TYR 0.018 0.002 TYR B 22 ARG 0.007 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 559 time to evaluate : 1.594 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: A 6 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7001 (ptp90) REVERT: A 68 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.3900 (tt) REVERT: A 171 MET cc_start: 0.6165 (mtm) cc_final: 0.5770 (mtt) REVERT: A 340 ASP cc_start: 0.8500 (m-30) cc_final: 0.8150 (m-30) REVERT: A 350 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7731 (ttpp) REVERT: A 365 PHE cc_start: 0.6679 (t80) cc_final: 0.6117 (t80) REVERT: A 427 LEU cc_start: 0.9231 (tt) cc_final: 0.8605 (tt) REVERT: A 497 MET cc_start: 0.8129 (mpt) cc_final: 0.7253 (mmt) REVERT: A 511 ASN cc_start: 0.8177 (t0) cc_final: 0.7933 (t0) REVERT: A 526 VAL cc_start: 0.9302 (t) cc_final: 0.8995 (p) REVERT: A 561 ASP cc_start: 0.7017 (t70) cc_final: 0.6717 (t70) REVERT: A 565 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8474 (mtmm) REVERT: A 619 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8040 (tmtt) REVERT: A 649 GLN cc_start: 0.8429 (pt0) cc_final: 0.8172 (pt0) REVERT: B 335 MET cc_start: 0.7270 (ttt) cc_final: 0.6958 (tpp) REVERT: B 336 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7602 (ttmm) REVERT: B 341 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7488 (p) REVERT: B 393 ILE cc_start: 0.9419 (tt) cc_final: 0.8046 (tt) REVERT: B 415 MET cc_start: 0.6892 (mtt) cc_final: 0.6642 (mtt) REVERT: B 490 LEU cc_start: 0.8837 (tp) cc_final: 0.8389 (tp) REVERT: B 574 MET cc_start: 0.6910 (mmm) cc_final: 0.6654 (tpt) REVERT: B 678 MET cc_start: 0.2874 (mmt) cc_final: 0.2091 (tpp) REVERT: B 685 TYR cc_start: 0.6774 (m-10) cc_final: 0.6495 (m-80) REVERT: B 715 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8313 (pp20) REVERT: C 9 LYS cc_start: 0.7809 (tttm) cc_final: 0.7215 (mttm) REVERT: C 13 ASN cc_start: 0.7450 (m-40) cc_final: 0.7084 (m-40) REVERT: C 69 GLU cc_start: 0.7184 (pt0) cc_final: 0.6854 (pp20) REVERT: C 81 ASP cc_start: 0.7285 (m-30) cc_final: 0.7040 (m-30) REVERT: C 190 PHE cc_start: 0.6241 (t80) cc_final: 0.5978 (t80) outliers start: 10 outliers final: 0 residues processed: 565 average time/residue: 0.2961 time to fit residues: 231.8277 Evaluate side-chains 326 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 0.0030 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 0.0050 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 70 ASN B 147 GLN B 154 GLN B 170 ASN B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14441 Z= 0.155 Angle : 0.590 8.570 19533 Z= 0.308 Chirality : 0.041 0.186 2142 Planarity : 0.005 0.064 2391 Dihedral : 12.618 175.252 2227 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.89 % 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: -3.25 (0.18), residues: 1653 helix: -1.40 (0.16), residues: 728 sheet: -1.12 (0.47), residues: 130 loop : -3.14 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 388 HIS 0.007 0.001 HIS A 41 PHE 0.028 0.001 PHE A 161 TYR 0.013 0.001 TYR C 715 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 410 time to evaluate : 1.601 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 196 MET cc_start: 0.7313 (ttp) cc_final: 0.6818 (ttm) REVERT: A 287 ILE cc_start: 0.9300 (mm) cc_final: 0.9095 (mm) REVERT: A 365 PHE cc_start: 0.6722 (t80) cc_final: 0.6154 (t80) REVERT: A 427 LEU cc_start: 0.9135 (tt) cc_final: 0.8720 (tt) REVERT: A 439 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7769 (tp30) REVERT: A 497 MET cc_start: 0.8202 (mpp) cc_final: 0.7727 (mmt) REVERT: A 511 ASN cc_start: 0.8454 (t0) cc_final: 0.8180 (t0) REVERT: A 514 LYS cc_start: 0.8795 (tttt) cc_final: 0.8574 (ttpp) REVERT: A 561 ASP cc_start: 0.7668 (t70) cc_final: 0.7456 (t70) REVERT: A 603 TRP cc_start: 0.6828 (m-90) cc_final: 0.6591 (m-90) REVERT: A 619 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7546 (tmtt) REVERT: A 649 GLN cc_start: 0.8405 (pt0) cc_final: 0.8099 (pt0) REVERT: A 677 ILE cc_start: 0.8176 (mt) cc_final: 0.7859 (mt) REVERT: B 93 LEU cc_start: 0.8948 (mt) cc_final: 0.8669 (mp) REVERT: B 130 GLN cc_start: 0.8507 (tp40) cc_final: 0.8247 (tt0) REVERT: B 289 SER cc_start: 0.8536 (m) cc_final: 0.8222 (p) REVERT: B 301 MET cc_start: 0.8078 (ttm) cc_final: 0.7748 (ttm) REVERT: B 336 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8136 (ttmm) REVERT: B 341 VAL cc_start: 0.7810 (p) cc_final: 0.7406 (p) REVERT: B 378 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: B 382 MET cc_start: 0.7645 (mtp) cc_final: 0.7409 (mmm) REVERT: B 383 ASN cc_start: 0.7399 (m110) cc_final: 0.7083 (m110) REVERT: B 423 MET cc_start: 0.8445 (mtm) cc_final: 0.8196 (mtm) REVERT: B 490 LEU cc_start: 0.8779 (tp) cc_final: 0.8366 (tp) REVERT: B 574 MET cc_start: 0.7414 (mmm) cc_final: 0.7174 (tpt) REVERT: B 624 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7229 (ttt180) REVERT: B 678 MET cc_start: 0.2575 (mmt) cc_final: 0.0916 (tpp) REVERT: C 17 ASP cc_start: 0.7062 (t0) cc_final: 0.6608 (t0) REVERT: C 62 MET cc_start: 0.7640 (ttm) cc_final: 0.7349 (ttp) REVERT: C 247 TRP cc_start: 0.8533 (p-90) cc_final: 0.8296 (p-90) REVERT: C 249 ILE cc_start: 0.8156 (tt) cc_final: 0.7954 (pt) outliers start: 2 outliers final: 0 residues processed: 411 average time/residue: 0.2901 time to fit residues: 166.8405 Evaluate side-chains 321 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 170 ASN A 207 ASN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14441 Z= 0.249 Angle : 0.634 7.637 19533 Z= 0.329 Chirality : 0.042 0.199 2142 Planarity : 0.004 0.057 2391 Dihedral : 12.524 177.467 2227 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.35 % Favored : 91.59 % Rotamer: Outliers : 0.14 % Allowed : 2.71 % Favored : 97.16 % 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: -2.31 (0.19), residues: 1653 helix: -0.40 (0.18), residues: 735 sheet: -0.98 (0.47), residues: 131 loop : -2.83 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 386 HIS 0.005 0.002 HIS C 216 PHE 0.016 0.001 PHE B 122 TYR 0.011 0.002 TYR B 22 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 370 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8891 (p) cc_final: 0.8444 (t) REVERT: A 170 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7184 (t0) REVERT: A 235 ARG cc_start: 0.6265 (tpm170) cc_final: 0.5868 (tpp-160) REVERT: A 365 PHE cc_start: 0.6863 (t80) cc_final: 0.6432 (t80) REVERT: A 427 LEU cc_start: 0.9151 (tt) cc_final: 0.8561 (tt) REVERT: A 439 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7962 (tp30) REVERT: A 497 MET cc_start: 0.8257 (mpp) cc_final: 0.7712 (mmt) REVERT: A 511 ASN cc_start: 0.8680 (t0) cc_final: 0.8403 (t0) REVERT: A 561 ASP cc_start: 0.7935 (t70) cc_final: 0.7684 (t70) REVERT: A 565 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8678 (mttm) REVERT: A 603 TRP cc_start: 0.7027 (m-90) cc_final: 0.6753 (m-90) REVERT: A 619 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7613 (tmtt) REVERT: A 649 GLN cc_start: 0.8419 (pt0) cc_final: 0.8114 (pt0) REVERT: B 1 MET cc_start: 0.7373 (tmm) cc_final: 0.7060 (tmm) REVERT: B 17 MET cc_start: 0.8490 (mmm) cc_final: 0.8160 (mmm) REVERT: B 93 LEU cc_start: 0.8895 (mt) cc_final: 0.8581 (mp) REVERT: B 123 SER cc_start: 0.8114 (p) cc_final: 0.7848 (p) REVERT: B 130 GLN cc_start: 0.8405 (tp40) cc_final: 0.7705 (tp40) REVERT: B 140 MET cc_start: 0.7536 (mmm) cc_final: 0.7133 (mmm) REVERT: B 254 SER cc_start: 0.9020 (p) cc_final: 0.8483 (t) REVERT: B 262 GLN cc_start: 0.8357 (tt0) cc_final: 0.8143 (tt0) REVERT: B 289 SER cc_start: 0.8395 (m) cc_final: 0.8116 (p) REVERT: B 301 MET cc_start: 0.7962 (ttm) cc_final: 0.7751 (ttm) REVERT: B 341 VAL cc_start: 0.7641 (p) cc_final: 0.7260 (p) REVERT: B 382 MET cc_start: 0.7741 (mtp) cc_final: 0.7525 (mmm) REVERT: B 423 MET cc_start: 0.8602 (mtm) cc_final: 0.8385 (mtm) REVERT: B 470 VAL cc_start: 0.9744 (m) cc_final: 0.9156 (t) REVERT: B 522 THR cc_start: 0.8505 (p) cc_final: 0.8157 (t) REVERT: B 574 MET cc_start: 0.7503 (mmm) cc_final: 0.7272 (tpt) REVERT: B 715 GLU cc_start: 0.8503 (pt0) cc_final: 0.8187 (pp20) REVERT: C 6 THR cc_start: 0.7692 (p) cc_final: 0.6661 (p) REVERT: C 9 LYS cc_start: 0.8143 (tttm) cc_final: 0.7673 (mttm) REVERT: C 247 TRP cc_start: 0.8716 (p-90) cc_final: 0.8425 (p-90) outliers start: 2 outliers final: 0 residues processed: 372 average time/residue: 0.2845 time to fit residues: 149.4041 Evaluate side-chains 288 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.0060 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14441 Z= 0.146 Angle : 0.565 9.788 19533 Z= 0.289 Chirality : 0.041 0.234 2142 Planarity : 0.004 0.056 2391 Dihedral : 12.424 176.717 2227 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.77 (0.20), residues: 1653 helix: 0.18 (0.19), residues: 740 sheet: -0.91 (0.49), residues: 121 loop : -2.64 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 386 HIS 0.003 0.001 HIS A 451 PHE 0.023 0.001 PHE B 524 TYR 0.008 0.001 TYR B 736 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.429 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 34 THR cc_start: 0.8851 (p) cc_final: 0.8344 (t) REVERT: A 196 MET cc_start: 0.8060 (ttp) cc_final: 0.7858 (ttm) REVERT: A 365 PHE cc_start: 0.6819 (t80) cc_final: 0.6451 (t80) REVERT: A 497 MET cc_start: 0.8175 (mpp) cc_final: 0.7535 (mmt) REVERT: A 511 ASN cc_start: 0.8571 (t0) cc_final: 0.8260 (t0) REVERT: A 561 ASP cc_start: 0.7960 (t70) cc_final: 0.7679 (t70) REVERT: A 619 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7896 (mmtp) REVERT: A 627 LEU cc_start: 0.9190 (mt) cc_final: 0.8892 (mt) REVERT: B 1 MET cc_start: 0.7506 (tmm) cc_final: 0.7228 (tmm) REVERT: B 130 GLN cc_start: 0.8453 (tp40) cc_final: 0.7748 (tp40) REVERT: B 140 MET cc_start: 0.7456 (mmm) cc_final: 0.7253 (mmm) REVERT: B 254 SER cc_start: 0.8999 (p) cc_final: 0.8414 (t) REVERT: B 289 SER cc_start: 0.8576 (m) cc_final: 0.8285 (p) REVERT: B 341 VAL cc_start: 0.7442 (p) cc_final: 0.7070 (p) REVERT: B 423 MET cc_start: 0.8513 (mtm) cc_final: 0.8211 (mtm) REVERT: B 479 SER cc_start: 0.8660 (t) cc_final: 0.8457 (t) REVERT: B 490 LEU cc_start: 0.8700 (tp) cc_final: 0.8394 (tp) REVERT: B 574 MET cc_start: 0.7406 (mmm) cc_final: 0.7198 (tpt) REVERT: B 624 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7237 (ttt180) REVERT: B 678 MET cc_start: 0.3321 (mmt) cc_final: 0.1697 (ttt) REVERT: B 715 GLU cc_start: 0.8347 (pt0) cc_final: 0.8068 (pp20) REVERT: C 6 THR cc_start: 0.7626 (p) cc_final: 0.7049 (p) REVERT: C 17 ASP cc_start: 0.6898 (t0) cc_final: 0.6663 (t0) REVERT: C 140 MET cc_start: 0.7914 (mtp) cc_final: 0.7680 (mtm) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2611 time to fit residues: 138.5149 Evaluate side-chains 293 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14441 Z= 0.204 Angle : 0.590 8.034 19533 Z= 0.306 Chirality : 0.042 0.250 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.406 177.176 2227 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -1.52 (0.20), residues: 1653 helix: 0.39 (0.19), residues: 738 sheet: -0.62 (0.50), residues: 119 loop : -2.54 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 386 HIS 0.004 0.001 HIS A 263 PHE 0.016 0.001 PHE B 524 TYR 0.017 0.001 TYR B 350 ARG 0.006 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8901 (p) cc_final: 0.8391 (t) REVERT: A 196 MET cc_start: 0.8078 (ttp) cc_final: 0.7625 (ttm) REVERT: A 365 PHE cc_start: 0.6973 (t80) cc_final: 0.6626 (t80) REVERT: A 427 LEU cc_start: 0.9068 (tt) cc_final: 0.8798 (mm) REVERT: A 497 MET cc_start: 0.8132 (mpp) cc_final: 0.7569 (mmt) REVERT: A 511 ASN cc_start: 0.8617 (t0) cc_final: 0.8333 (t0) REVERT: A 561 ASP cc_start: 0.8077 (t70) cc_final: 0.7828 (t70) REVERT: A 619 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7958 (mmtp) REVERT: B 96 MET cc_start: 0.7315 (mpp) cc_final: 0.6674 (mtt) REVERT: B 123 SER cc_start: 0.7949 (p) cc_final: 0.7648 (p) REVERT: B 130 GLN cc_start: 0.8455 (tp40) cc_final: 0.7768 (tp40) REVERT: B 254 SER cc_start: 0.9050 (p) cc_final: 0.8417 (t) REVERT: B 289 SER cc_start: 0.8517 (m) cc_final: 0.8196 (p) REVERT: B 335 MET cc_start: 0.7266 (tpp) cc_final: 0.7018 (tpp) REVERT: B 341 VAL cc_start: 0.7569 (p) cc_final: 0.7204 (p) REVERT: B 415 MET cc_start: 0.7044 (mtt) cc_final: 0.6746 (mtt) REVERT: B 423 MET cc_start: 0.8395 (mtm) cc_final: 0.8103 (mtm) REVERT: B 470 VAL cc_start: 0.9718 (m) cc_final: 0.9482 (t) REVERT: B 479 SER cc_start: 0.8652 (t) cc_final: 0.8411 (t) REVERT: B 522 THR cc_start: 0.8480 (p) cc_final: 0.8137 (t) REVERT: B 574 MET cc_start: 0.7485 (mmm) cc_final: 0.7064 (tpt) REVERT: B 604 SER cc_start: 0.9000 (m) cc_final: 0.8500 (p) REVERT: B 678 MET cc_start: 0.2813 (mmt) cc_final: 0.1160 (ttt) REVERT: B 715 GLU cc_start: 0.8549 (pt0) cc_final: 0.8195 (pp20) REVERT: C 6 THR cc_start: 0.7661 (p) cc_final: 0.7104 (p) REVERT: C 234 GLU cc_start: 0.7134 (pm20) cc_final: 0.6823 (pm20) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2636 time to fit residues: 133.1296 Evaluate side-chains 275 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14441 Z= 0.165 Angle : 0.575 8.122 19533 Z= 0.295 Chirality : 0.041 0.207 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.366 177.263 2227 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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 (0.21), residues: 1653 helix: 0.59 (0.19), residues: 741 sheet: -0.53 (0.50), residues: 119 loop : -2.48 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 386 HIS 0.003 0.001 HIS A 451 PHE 0.036 0.001 PHE A 161 TYR 0.017 0.001 TYR A 419 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8909 (p) cc_final: 0.8419 (t) REVERT: A 365 PHE cc_start: 0.7024 (t80) cc_final: 0.6583 (t80) REVERT: A 497 MET cc_start: 0.8041 (mpp) cc_final: 0.7449 (mmt) REVERT: A 511 ASN cc_start: 0.8588 (t0) cc_final: 0.8316 (t0) REVERT: A 603 TRP cc_start: 0.6824 (m-90) cc_final: 0.6472 (m-90) REVERT: A 619 LYS cc_start: 0.8405 (mmtt) cc_final: 0.7875 (mmtp) REVERT: B 17 MET cc_start: 0.8428 (mmm) cc_final: 0.8084 (mmm) REVERT: B 123 SER cc_start: 0.7956 (p) cc_final: 0.7550 (p) REVERT: B 130 GLN cc_start: 0.8483 (tp40) cc_final: 0.7742 (tp40) REVERT: B 140 MET cc_start: 0.7582 (mmm) cc_final: 0.7089 (mmm) REVERT: B 254 SER cc_start: 0.8962 (p) cc_final: 0.8389 (t) REVERT: B 289 SER cc_start: 0.8400 (m) cc_final: 0.8063 (p) REVERT: B 341 VAL cc_start: 0.7437 (p) cc_final: 0.7121 (p) REVERT: B 381 LEU cc_start: 0.7684 (mp) cc_final: 0.6968 (mp) REVERT: B 423 MET cc_start: 0.8506 (mtm) cc_final: 0.8204 (mtm) REVERT: B 470 VAL cc_start: 0.9703 (m) cc_final: 0.9439 (t) REVERT: B 479 SER cc_start: 0.8661 (t) cc_final: 0.8423 (t) REVERT: B 490 LEU cc_start: 0.8790 (tp) cc_final: 0.8584 (tp) REVERT: B 522 THR cc_start: 0.8517 (p) cc_final: 0.8222 (t) REVERT: B 574 MET cc_start: 0.7517 (mmm) cc_final: 0.7072 (tpt) REVERT: B 715 GLU cc_start: 0.8508 (pt0) cc_final: 0.8179 (pp20) REVERT: B 717 LYS cc_start: 0.8482 (tppt) cc_final: 0.8252 (tppt) REVERT: C 6 THR cc_start: 0.7646 (p) cc_final: 0.6988 (p) REVERT: C 17 ASP cc_start: 0.6716 (t0) cc_final: 0.6492 (t0) REVERT: C 234 GLU cc_start: 0.7119 (pm20) cc_final: 0.6899 (pm20) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.2567 time to fit residues: 134.6130 Evaluate side-chains 276 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 0.0570 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 14441 Z= 0.157 Angle : 0.572 7.391 19533 Z= 0.292 Chirality : 0.041 0.240 2142 Planarity : 0.004 0.055 2391 Dihedral : 12.339 177.274 2227 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1653 helix: 0.69 (0.19), residues: 741 sheet: -0.47 (0.50), residues: 119 loop : -2.42 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 247 HIS 0.003 0.001 HIS A 31 PHE 0.032 0.001 PHE B 89 TYR 0.021 0.001 TYR A 419 ARG 0.006 0.000 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8897 (p) cc_final: 0.8399 (t) REVERT: A 43 GLN cc_start: 0.8256 (tp40) cc_final: 0.8052 (tp40) REVERT: A 365 PHE cc_start: 0.6960 (t80) cc_final: 0.6671 (t80) REVERT: A 497 MET cc_start: 0.7982 (mpp) cc_final: 0.7418 (mmt) REVERT: A 511 ASN cc_start: 0.8582 (t0) cc_final: 0.8272 (t0) REVERT: A 561 ASP cc_start: 0.7823 (t70) cc_final: 0.7436 (t0) REVERT: A 603 TRP cc_start: 0.6782 (m-90) cc_final: 0.6442 (m-90) REVERT: A 619 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7802 (mmtp) REVERT: A 627 LEU cc_start: 0.9243 (mt) cc_final: 0.8996 (mt) REVERT: A 650 LYS cc_start: 0.8416 (mtmm) cc_final: 0.7906 (ptpp) REVERT: B 96 MET cc_start: 0.6952 (mpp) cc_final: 0.6406 (mtt) REVERT: B 123 SER cc_start: 0.7957 (p) cc_final: 0.7622 (p) REVERT: B 130 GLN cc_start: 0.8483 (tp40) cc_final: 0.7734 (tp40) REVERT: B 140 MET cc_start: 0.7514 (mmm) cc_final: 0.7056 (mmm) REVERT: B 220 ILE cc_start: 0.9267 (mm) cc_final: 0.9028 (tp) REVERT: B 254 SER cc_start: 0.8997 (p) cc_final: 0.8346 (t) REVERT: B 289 SER cc_start: 0.8457 (m) cc_final: 0.8120 (p) REVERT: B 341 VAL cc_start: 0.7638 (p) cc_final: 0.7325 (p) REVERT: B 423 MET cc_start: 0.8417 (mtm) cc_final: 0.8082 (mtm) REVERT: B 428 ARG cc_start: 0.7290 (mmp-170) cc_final: 0.6950 (mmp80) REVERT: B 470 VAL cc_start: 0.9706 (m) cc_final: 0.9468 (t) REVERT: B 490 LEU cc_start: 0.8756 (tp) cc_final: 0.8448 (tt) REVERT: B 574 MET cc_start: 0.7513 (mmm) cc_final: 0.7076 (tpt) REVERT: B 678 MET cc_start: 0.3144 (mmt) cc_final: 0.1213 (ttt) REVERT: B 715 GLU cc_start: 0.8528 (pt0) cc_final: 0.8203 (pp20) REVERT: B 717 LYS cc_start: 0.8453 (tppt) cc_final: 0.8237 (tppt) REVERT: C 6 THR cc_start: 0.7604 (p) cc_final: 0.6949 (p) REVERT: C 49 LEU cc_start: 0.8297 (tp) cc_final: 0.8035 (tp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2609 time to fit residues: 133.0490 Evaluate side-chains 278 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14441 Z= 0.150 Angle : 0.580 9.615 19533 Z= 0.296 Chirality : 0.041 0.262 2142 Planarity : 0.004 0.053 2391 Dihedral : 12.303 177.311 2227 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -1.12 (0.21), residues: 1653 helix: 0.77 (0.19), residues: 747 sheet: -0.45 (0.50), residues: 119 loop : -2.40 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 357 HIS 0.010 0.001 HIS A 277 PHE 0.023 0.001 PHE C 35 TYR 0.020 0.001 TYR A 419 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8888 (p) cc_final: 0.8414 (t) REVERT: A 43 GLN cc_start: 0.8419 (tp40) cc_final: 0.8156 (tp40) REVERT: A 345 ILE cc_start: 0.8409 (mm) cc_final: 0.8188 (mm) REVERT: A 365 PHE cc_start: 0.6896 (t80) cc_final: 0.6624 (t80) REVERT: A 416 MET cc_start: 0.7975 (ppp) cc_final: 0.6930 (ppp) REVERT: A 497 MET cc_start: 0.7926 (mpp) cc_final: 0.7372 (mmt) REVERT: A 511 ASN cc_start: 0.8589 (t0) cc_final: 0.8305 (t0) REVERT: A 561 ASP cc_start: 0.7814 (t70) cc_final: 0.7238 (t0) REVERT: A 603 TRP cc_start: 0.6741 (m-90) cc_final: 0.6397 (m-90) REVERT: A 619 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7754 (mmtp) REVERT: A 627 LEU cc_start: 0.9245 (mt) cc_final: 0.9020 (mt) REVERT: A 677 ILE cc_start: 0.8239 (mt) cc_final: 0.7832 (mt) REVERT: B 79 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 130 GLN cc_start: 0.8475 (tp40) cc_final: 0.7680 (tp40) REVERT: B 140 MET cc_start: 0.7518 (mmm) cc_final: 0.7068 (mmm) REVERT: B 220 ILE cc_start: 0.9246 (mm) cc_final: 0.9014 (tp) REVERT: B 254 SER cc_start: 0.9019 (p) cc_final: 0.8405 (t) REVERT: B 289 SER cc_start: 0.8437 (m) cc_final: 0.8103 (p) REVERT: B 341 VAL cc_start: 0.7596 (p) cc_final: 0.7273 (p) REVERT: B 423 MET cc_start: 0.8445 (mtm) cc_final: 0.8084 (mtm) REVERT: B 428 ARG cc_start: 0.7409 (mmp-170) cc_final: 0.7058 (mmp80) REVERT: B 479 SER cc_start: 0.8719 (t) cc_final: 0.8475 (t) REVERT: B 490 LEU cc_start: 0.8718 (tp) cc_final: 0.8483 (tp) REVERT: B 522 THR cc_start: 0.8614 (p) cc_final: 0.8293 (t) REVERT: B 574 MET cc_start: 0.7543 (mmm) cc_final: 0.7088 (tpt) REVERT: B 678 MET cc_start: 0.3018 (mmt) cc_final: 0.1097 (ttt) REVERT: B 715 GLU cc_start: 0.8529 (pt0) cc_final: 0.8209 (pp20) REVERT: C 6 THR cc_start: 0.7586 (p) cc_final: 0.6968 (p) REVERT: C 49 LEU cc_start: 0.8320 (tp) cc_final: 0.7973 (tp) REVERT: C 739 PHE cc_start: 0.7328 (t80) cc_final: 0.6940 (t80) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2593 time to fit residues: 127.9269 Evaluate side-chains 273 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.0970 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 0.0010 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 299 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14441 Z= 0.152 Angle : 0.587 7.531 19533 Z= 0.299 Chirality : 0.041 0.255 2142 Planarity : 0.004 0.051 2391 Dihedral : 12.281 177.394 2227 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -1.10 (0.21), residues: 1653 helix: 0.72 (0.19), residues: 752 sheet: -0.43 (0.50), residues: 119 loop : -2.34 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 247 HIS 0.003 0.001 HIS A 263 PHE 0.022 0.001 PHE B 726 TYR 0.022 0.001 TYR A 419 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8414 (tp40) cc_final: 0.8150 (tp40) REVERT: A 235 ARG cc_start: 0.6358 (tpm170) cc_final: 0.5914 (tpm170) REVERT: A 365 PHE cc_start: 0.6835 (t80) cc_final: 0.6588 (t80) REVERT: A 497 MET cc_start: 0.7877 (mpp) cc_final: 0.7264 (mmt) REVERT: A 511 ASN cc_start: 0.8581 (t0) cc_final: 0.8312 (t0) REVERT: A 561 ASP cc_start: 0.7818 (t70) cc_final: 0.7177 (t0) REVERT: A 573 THR cc_start: 0.8508 (m) cc_final: 0.8240 (t) REVERT: A 603 TRP cc_start: 0.6708 (m-90) cc_final: 0.6410 (m-90) REVERT: A 619 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7784 (mmtp) REVERT: B 130 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8332 (tp-100) REVERT: B 150 VAL cc_start: 0.9107 (t) cc_final: 0.8837 (m) REVERT: B 220 ILE cc_start: 0.9230 (mm) cc_final: 0.9009 (tp) REVERT: B 254 SER cc_start: 0.9198 (p) cc_final: 0.8574 (t) REVERT: B 289 SER cc_start: 0.8554 (m) cc_final: 0.8180 (p) REVERT: B 341 VAL cc_start: 0.7565 (p) cc_final: 0.7247 (p) REVERT: B 423 MET cc_start: 0.8327 (mtm) cc_final: 0.8009 (mtm) REVERT: B 479 SER cc_start: 0.8435 (t) cc_final: 0.8207 (t) REVERT: B 490 LEU cc_start: 0.8805 (tp) cc_final: 0.8503 (tp) REVERT: B 522 THR cc_start: 0.8676 (p) cc_final: 0.8359 (t) REVERT: B 574 MET cc_start: 0.7390 (mmm) cc_final: 0.6883 (tpt) REVERT: B 678 MET cc_start: 0.2814 (mmt) cc_final: 0.0956 (ttt) REVERT: B 692 TYR cc_start: 0.7134 (t80) cc_final: 0.6886 (t80) REVERT: B 715 GLU cc_start: 0.8472 (pt0) cc_final: 0.8095 (pp20) REVERT: C 6 THR cc_start: 0.7410 (p) cc_final: 0.6777 (p) REVERT: C 49 LEU cc_start: 0.8344 (tp) cc_final: 0.8037 (tp) REVERT: C 171 MET cc_start: 0.7404 (mtp) cc_final: 0.6960 (ptm) REVERT: C 247 TRP cc_start: 0.8480 (p-90) cc_final: 0.8202 (p-90) REVERT: C 739 PHE cc_start: 0.7431 (t80) cc_final: 0.7074 (t80) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2626 time to fit residues: 129.7812 Evaluate side-chains 281 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.0170 chunk 141 optimal weight: 0.0370 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 515 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14441 Z= 0.179 Angle : 0.614 10.943 19533 Z= 0.312 Chirality : 0.042 0.261 2142 Planarity : 0.004 0.050 2391 Dihedral : 12.284 177.646 2227 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.44 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % 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: -1.10 (0.21), residues: 1653 helix: 0.74 (0.19), residues: 750 sheet: -0.49 (0.50), residues: 119 loop : -2.34 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 357 HIS 0.008 0.001 HIS A 277 PHE 0.020 0.001 PHE B 726 TYR 0.023 0.001 TYR B 350 ARG 0.005 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.677 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 34 THR cc_start: 0.8914 (p) cc_final: 0.8446 (t) REVERT: A 43 GLN cc_start: 0.8409 (tp40) cc_final: 0.8138 (tp40) REVERT: A 365 PHE cc_start: 0.6887 (t80) cc_final: 0.6448 (t80) REVERT: A 497 MET cc_start: 0.7981 (mpp) cc_final: 0.7382 (mmt) REVERT: A 511 ASN cc_start: 0.8587 (t0) cc_final: 0.8342 (t0) REVERT: A 561 ASP cc_start: 0.7798 (t70) cc_final: 0.7187 (t70) REVERT: A 603 TRP cc_start: 0.6738 (m-90) cc_final: 0.6495 (m-90) REVERT: A 619 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7900 (mmtp) REVERT: B 96 MET cc_start: 0.6930 (mpp) cc_final: 0.6187 (mpp) REVERT: B 123 SER cc_start: 0.7987 (p) cc_final: 0.7681 (p) REVERT: B 130 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8306 (tp-100) REVERT: B 150 VAL cc_start: 0.9136 (t) cc_final: 0.8907 (m) REVERT: B 254 SER cc_start: 0.9231 (p) cc_final: 0.8573 (t) REVERT: B 289 SER cc_start: 0.8694 (m) cc_final: 0.8330 (p) REVERT: B 337 ASP cc_start: 0.8023 (m-30) cc_final: 0.7763 (m-30) REVERT: B 341 VAL cc_start: 0.7569 (p) cc_final: 0.7297 (p) REVERT: B 423 MET cc_start: 0.8454 (mtm) cc_final: 0.8058 (mtm) REVERT: B 479 SER cc_start: 0.8587 (t) cc_final: 0.8356 (t) REVERT: B 490 LEU cc_start: 0.8756 (tp) cc_final: 0.8352 (tt) REVERT: B 522 THR cc_start: 0.8542 (p) cc_final: 0.8214 (t) REVERT: B 574 MET cc_start: 0.7663 (mmm) cc_final: 0.7263 (tpt) REVERT: B 678 MET cc_start: 0.2383 (mmt) cc_final: 0.0506 (ttt) REVERT: B 692 TYR cc_start: 0.7200 (t80) cc_final: 0.6892 (t80) REVERT: B 715 GLU cc_start: 0.8519 (pt0) cc_final: 0.8084 (pp20) REVERT: C 6 THR cc_start: 0.7380 (p) cc_final: 0.6762 (p) REVERT: C 49 LEU cc_start: 0.8430 (tp) cc_final: 0.7907 (tp) REVERT: C 51 MET cc_start: 0.8503 (tpp) cc_final: 0.7827 (tpp) REVERT: C 171 MET cc_start: 0.7467 (mtp) cc_final: 0.6932 (ptm) REVERT: C 247 TRP cc_start: 0.8438 (p-90) cc_final: 0.8192 (p-90) REVERT: C 739 PHE cc_start: 0.7474 (t80) cc_final: 0.7142 (t80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2505 time to fit residues: 121.2868 Evaluate side-chains 269 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.158677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127852 restraints weight = 25843.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129652 restraints weight = 15055.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131151 restraints weight = 10584.725| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14441 Z= 0.168 Angle : 0.617 10.941 19533 Z= 0.311 Chirality : 0.042 0.257 2142 Planarity : 0.004 0.050 2391 Dihedral : 12.277 177.710 2227 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.07 (0.21), residues: 1653 helix: 0.72 (0.19), residues: 752 sheet: -0.48 (0.48), residues: 131 loop : -2.30 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 357 HIS 0.003 0.001 HIS A 263 PHE 0.020 0.001 PHE B 726 TYR 0.020 0.001 TYR B 350 ARG 0.006 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.38 seconds wall clock time: 59 minutes 58.54 seconds (3598.54 seconds total)