Starting phenix.real_space_refine on Thu Mar 21 21:18:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9c_14570/03_2024/7z9c_14570_trim_updated.pdb" } resolution = 3.06 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= 0.028 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: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9823 2.51 5 N 2835 2.21 5 O 3184 1.98 5 H 15359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 31325 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'BWH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 14.29, per 1000 atoms: 0.46 Number of scatterers: 31325 At special positions: 0 Unit cell: (126.42, 139.32, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3184 8.00 N 2835 7.00 C 9823 6.00 H 15359 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.30 Conformation dependent library (CDL) restraints added in 3.1 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 22 sheets defined 44.0% alpha, 9.1% beta 12 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 15.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.580A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.534A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.576A pdb=" N GLU A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.621A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.625A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.703A pdb=" N ALA A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA A 422 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 423 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 424' Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 468 through 493 removed outlier: 3.652A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.717A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 463' Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.877A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.795A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 797 through 800 No H-bonds generated for 'chain 'B' and resid 797 through 800' Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.536A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.607A pdb=" N GLU C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.738A pdb=" N ASN C 319 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 398 removed outlier: 3.665A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 418 through 427 removed outlier: 4.002A pdb=" N ALA C 421 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C 422 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 468 through 493 removed outlier: 4.010A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.583A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 578 through 597 removed outlier: 3.719A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 617 through 619 No H-bonds generated for 'chain 'D' and resid 617 through 619' Processing helix chain 'D' and resid 626 through 639 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.643A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 785 through 794 Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= D, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.778A pdb=" N GLU A 520 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= F, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.703A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= H, first strand: chain 'B' and resid 419 through 421 removed outlier: 6.730A pdb=" N SER B 492 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 528 through 530 Processing sheet with id= J, first strand: chain 'B' and resid 542 through 546 removed outlier: 4.042A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= L, first strand: chain 'B' and resid 651 through 653 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 171 through 174 Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 4.022A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 246 through 249 Processing sheet with id= R, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= S, first strand: chain 'D' and resid 419 through 421 removed outlier: 6.843A pdb=" N SER D 492 " --> pdb=" O LEU D 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 528 through 530 Processing sheet with id= U, first strand: chain 'D' and resid 543 through 546 Processing sheet with id= V, first strand: chain 'D' and resid 646 through 652 592 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 24.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15351 1.03 - 1.23: 35 1.23 - 1.42: 6716 1.42 - 1.61: 9501 1.61 - 1.81: 108 Bond restraints: 31711 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.611 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C41 BWH C 901 " pdb=" O6 BWH C 901 " ideal model delta sigma weight residual 1.233 1.303 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C41 BWH C 901 " pdb=" O7 BWH C 901 " ideal model delta sigma weight residual 1.274 1.220 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" O1P PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.522 1.478 0.044 2.00e-02 2.50e+03 4.87e+00 ... (remaining 31706 not shown) Histogram of bond angle deviations from ideal: 100.40 - 115.98: 41225 115.98 - 131.56: 16180 131.56 - 147.14: 35 147.14 - 162.73: 0 162.73 - 178.31: 1 Bond angle restraints: 57441 Sorted by residual: angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 110.62 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.62 -9.70 3.00e+00 1.11e-01 1.04e+01 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 116.15 -4.65 1.50e+00 4.44e-01 9.59e+00 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 115.93 -4.43 1.50e+00 4.44e-01 8.73e+00 angle pdb=" O PTR A 122 " pdb=" C PTR A 122 " pdb=" N THR A 123 " ideal model delta sigma weight residual 123.00 118.98 4.02 1.60e+00 3.91e-01 6.31e+00 ... (remaining 57436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 13757 26.48 - 52.96: 591 52.96 - 79.44: 117 79.44 - 105.92: 5 105.92 - 132.40: 2 Dihedral angle restraints: 14472 sinusoidal: 8498 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP A 297 " pdb=" C ASP A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 14469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1706 0.035 - 0.069: 572 0.069 - 0.104: 129 0.104 - 0.139: 86 0.139 - 0.173: 10 Chirality restraints: 2503 Sorted by residual: chirality pdb=" C17 BWH C 901 " pdb=" C18 BWH C 901 " pdb=" C20 BWH C 901 " pdb=" N1 BWH C 901 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 BWH C 901 " -0.122 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C16 BWH C 901 " 0.044 2.00e-02 2.50e+03 pdb=" C17 BWH C 901 " -0.164 2.00e-02 2.50e+03 pdb=" N1 BWH C 901 " 0.216 2.00e-02 2.50e+03 pdb=" O2 BWH C 901 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C35 BWH C 901 " -0.033 2.00e-02 2.50e+03 9.07e-02 2.05e+02 pdb=" C36 BWH C 901 " -0.076 2.00e-02 2.50e+03 pdb=" C37 BWH C 901 " -0.057 2.00e-02 2.50e+03 pdb=" C38 BWH C 901 " 0.010 2.00e-02 2.50e+03 pdb=" C39 BWH C 901 " 0.054 2.00e-02 2.50e+03 pdb=" C40 BWH C 901 " 0.034 2.00e-02 2.50e+03 pdb=" C41 BWH C 901 " 0.039 2.00e-02 2.50e+03 pdb=" N5 BWH C 901 " -0.087 2.00e-02 2.50e+03 pdb=" O8 BWH C 901 " -0.102 2.00e-02 2.50e+03 pdb=" O9 BWH C 901 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 BWH C 901 " 0.044 2.00e-02 2.50e+03 8.28e-02 1.71e+02 pdb=" C29 BWH C 901 " 0.083 2.00e-02 2.50e+03 pdb=" C30 BWH C 901 " 0.058 2.00e-02 2.50e+03 pdb=" C31 BWH C 901 " -0.006 2.00e-02 2.50e+03 pdb=" C32 BWH C 901 " -0.031 2.00e-02 2.50e+03 pdb=" C33 BWH C 901 " -0.006 2.00e-02 2.50e+03 pdb=" C34 BWH C 901 " -0.076 2.00e-02 2.50e+03 pdb=" N4 BWH C 901 " 0.029 2.00e-02 2.50e+03 pdb=" O10 BWH C 901 " 0.101 2.00e-02 2.50e+03 pdb=" O11 BWH C 901 " -0.196 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 5742 2.31 - 2.88: 69144 2.88 - 3.45: 70914 3.45 - 4.03: 99420 4.03 - 4.60: 154589 Nonbonded interactions: 399809 Sorted by model distance: nonbonded pdb=" O GLN B 591 " pdb="HD22 ASN B 595 " model vdw 1.737 1.850 nonbonded pdb=" O HIS D 679 " pdb=" HG1 THR D 683 " model vdw 1.739 1.850 nonbonded pdb=" O LEU C 320 " pdb=" HG1 THR C 324 " model vdw 1.740 1.850 nonbonded pdb=" HH TYR D 545 " pdb=" OE2 GLU D 752 " model vdw 1.743 1.850 nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.745 1.850 ... (remaining 399804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 8 through 524) } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.460 Extract box with map and model: 14.760 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 106.220 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 16352 Z= 0.266 Angle : 0.613 10.704 22380 Z= 0.323 Chirality : 0.041 0.173 2503 Planarity : 0.006 0.135 2710 Dihedral : 14.024 132.401 6404 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % 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: 0.45 (0.20), residues: 1824 helix: 2.30 (0.18), residues: 827 sheet: -0.47 (0.39), residues: 176 loop : -1.74 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS A 339 PHE 0.008 0.001 PHE C 368 TYR 0.011 0.001 TYR C 266 ARG 0.002 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.160 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: B 781 MET cc_start: 0.8788 (mmt) cc_final: 0.8287 (mmt) REVERT: C 338 HIS cc_start: 0.7471 (t-90) cc_final: 0.7246 (t-90) REVERT: D 592 LYS cc_start: 0.8644 (tppp) cc_final: 0.8392 (mmtt) REVERT: D 600 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6698 (mmm160) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.8007 time to fit residues: 264.1236 Evaluate side-chains 138 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS B 595 ASN B 631 ASN D 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16352 Z= 0.216 Angle : 0.494 5.383 22380 Z= 0.277 Chirality : 0.040 0.145 2503 Planarity : 0.004 0.051 2710 Dihedral : 16.029 138.478 2752 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 0.52 % Allowed : 5.16 % Favored : 94.32 % 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: 0.59 (0.20), residues: 1824 helix: 2.52 (0.18), residues: 827 sheet: -0.52 (0.39), residues: 176 loop : -1.77 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.006 0.001 HIS D 643 PHE 0.006 0.001 PHE C 330 TYR 0.011 0.001 TYR C 266 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 2.493 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: B 781 MET cc_start: 0.8781 (mmt) cc_final: 0.8261 (mmt) REVERT: D 480 ARG cc_start: 0.6435 (mmm160) cc_final: 0.6231 (mmt90) REVERT: D 592 LYS cc_start: 0.8642 (tppp) cc_final: 0.8372 (mmtt) REVERT: D 600 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6713 (mmm160) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.7764 time to fit residues: 164.2344 Evaluate side-chains 131 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16352 Z= 0.194 Angle : 0.480 4.615 22380 Z= 0.269 Chirality : 0.039 0.144 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.058 138.410 2752 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.65 % Allowed : 6.06 % Favored : 93.29 % 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: 0.57 (0.20), residues: 1824 helix: 2.49 (0.18), residues: 828 sheet: -0.54 (0.38), residues: 185 loop : -1.78 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS D 643 PHE 0.006 0.001 PHE C 330 TYR 0.011 0.001 TYR C 266 ARG 0.003 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 781 MET cc_start: 0.8765 (mmt) cc_final: 0.8248 (mmt) REVERT: D 592 LYS cc_start: 0.8658 (tppp) cc_final: 0.8361 (mmtt) REVERT: D 600 ARG cc_start: 0.7285 (mtm110) cc_final: 0.6689 (mmm160) outliers start: 10 outliers final: 7 residues processed: 136 average time/residue: 0.7523 time to fit residues: 146.3708 Evaluate side-chains 129 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN B 631 ASN C 399 HIS D 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16352 Z= 0.278 Angle : 0.525 5.702 22380 Z= 0.295 Chirality : 0.041 0.155 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.332 138.987 2752 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 0.97 % Allowed : 6.58 % Favored : 92.45 % 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: 0.29 (0.20), residues: 1824 helix: 2.21 (0.18), residues: 834 sheet: -0.65 (0.38), residues: 185 loop : -1.90 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 725 HIS 0.006 0.001 HIS D 643 PHE 0.009 0.001 PHE C 330 TYR 0.012 0.001 TYR C 266 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 781 MET cc_start: 0.8799 (mmt) cc_final: 0.8294 (mmt) REVERT: D 592 LYS cc_start: 0.8688 (tppp) cc_final: 0.8378 (mmtt) REVERT: D 600 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6730 (mmm160) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.7279 time to fit residues: 143.0389 Evaluate side-chains 128 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 0.0470 chunk 45 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16352 Z= 0.174 Angle : 0.470 4.283 22380 Z= 0.265 Chirality : 0.039 0.143 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.276 141.160 2752 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.84 % Allowed : 6.84 % Favored : 92.32 % 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: 0.48 (0.20), residues: 1824 helix: 2.44 (0.18), residues: 829 sheet: -0.66 (0.38), residues: 180 loop : -1.82 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS D 643 PHE 0.006 0.001 PHE C 368 TYR 0.010 0.001 TYR C 266 ARG 0.006 0.000 ARG D 689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 781 MET cc_start: 0.8760 (mmt) cc_final: 0.8279 (mmt) REVERT: D 592 LYS cc_start: 0.8695 (tppp) cc_final: 0.8362 (mmtt) REVERT: D 600 ARG cc_start: 0.7362 (mtm110) cc_final: 0.6692 (mmm160) outliers start: 13 outliers final: 11 residues processed: 128 average time/residue: 0.7445 time to fit residues: 134.5078 Evaluate side-chains 127 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16352 Z= 0.257 Angle : 0.505 5.377 22380 Z= 0.284 Chirality : 0.040 0.152 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.405 139.245 2752 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 0.97 % Allowed : 6.90 % Favored : 92.13 % 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: 0.32 (0.20), residues: 1824 helix: 2.29 (0.18), residues: 829 sheet: -0.65 (0.38), residues: 185 loop : -1.93 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS D 643 PHE 0.008 0.001 PHE C 330 TYR 0.011 0.001 TYR C 266 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 781 MET cc_start: 0.8769 (mmt) cc_final: 0.8285 (mmt) REVERT: D 592 LYS cc_start: 0.8717 (tppp) cc_final: 0.8365 (mmtt) REVERT: D 600 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6807 (mmm160) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 0.7511 time to fit residues: 138.2821 Evaluate side-chains 129 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16352 Z= 0.141 Angle : 0.450 5.069 22380 Z= 0.254 Chirality : 0.039 0.138 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.306 142.469 2752 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 0.84 % Allowed : 7.42 % Favored : 91.74 % 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: 0.63 (0.20), residues: 1824 helix: 2.58 (0.18), residues: 828 sheet: -0.62 (0.38), residues: 180 loop : -1.75 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.003 0.000 HIS C 399 PHE 0.005 0.001 PHE C 368 TYR 0.007 0.001 TYR C 266 ARG 0.002 0.000 ARG D 667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 587 TYR cc_start: 0.6350 (t80) cc_final: 0.5913 (t80) REVERT: B 781 MET cc_start: 0.8685 (mmt) cc_final: 0.8175 (mmt) REVERT: D 592 LYS cc_start: 0.8716 (tppp) cc_final: 0.8372 (mmtt) REVERT: D 600 ARG cc_start: 0.7386 (mtm110) cc_final: 0.6729 (mmm160) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.7465 time to fit residues: 136.3761 Evaluate side-chains 129 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16352 Z= 0.179 Angle : 0.463 4.413 22380 Z= 0.260 Chirality : 0.039 0.142 2503 Planarity : 0.004 0.047 2710 Dihedral : 16.328 139.760 2752 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 0.84 % Allowed : 7.68 % Favored : 91.48 % 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: 0.59 (0.20), residues: 1824 helix: 2.55 (0.18), residues: 830 sheet: -0.61 (0.38), residues: 180 loop : -1.81 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS D 643 PHE 0.007 0.001 PHE C 368 TYR 0.009 0.001 TYR C 266 ARG 0.002 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.853 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: B 587 TYR cc_start: 0.6378 (t80) cc_final: 0.5944 (t80) REVERT: B 781 MET cc_start: 0.8715 (mmt) cc_final: 0.8251 (mmt) REVERT: D 592 LYS cc_start: 0.8719 (tppp) cc_final: 0.8365 (mmtt) REVERT: D 600 ARG cc_start: 0.7405 (mtm110) cc_final: 0.6734 (mmm160) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.7210 time to fit residues: 132.3816 Evaluate side-chains 129 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16352 Z= 0.253 Angle : 0.503 5.255 22380 Z= 0.282 Chirality : 0.040 0.151 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.463 140.344 2752 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.31 % Rotamer: Outliers : 0.97 % Allowed : 7.55 % Favored : 91.48 % 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: 0.40 (0.20), residues: 1824 helix: 2.38 (0.18), residues: 829 sheet: -0.64 (0.38), residues: 180 loop : -1.90 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 629 HIS 0.004 0.001 HIS D 643 PHE 0.008 0.001 PHE C 330 TYR 0.011 0.001 TYR C 266 ARG 0.003 0.000 ARG B 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 2.386 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: B 587 TYR cc_start: 0.6423 (t80) cc_final: 0.5996 (t80) REVERT: B 781 MET cc_start: 0.8753 (mmt) cc_final: 0.8287 (mmt) REVERT: D 592 LYS cc_start: 0.8728 (tppp) cc_final: 0.8376 (mmtt) REVERT: D 600 ARG cc_start: 0.7496 (mtm110) cc_final: 0.6756 (mmm160) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.7127 time to fit residues: 132.4076 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16352 Z= 0.145 Angle : 0.447 4.198 22380 Z= 0.252 Chirality : 0.039 0.141 2503 Planarity : 0.004 0.047 2710 Dihedral : 16.330 142.561 2752 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 0.77 % Allowed : 7.74 % Favored : 91.48 % 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: 0.69 (0.20), residues: 1824 helix: 2.63 (0.18), residues: 828 sheet: -0.66 (0.36), residues: 198 loop : -1.72 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 629 HIS 0.003 0.001 HIS C 262 PHE 0.005 0.001 PHE C 368 TYR 0.007 0.001 TYR C 21 ARG 0.002 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 587 TYR cc_start: 0.6256 (t80) cc_final: 0.5872 (t80) REVERT: B 781 MET cc_start: 0.8670 (mmt) cc_final: 0.8166 (mmt) REVERT: D 592 LYS cc_start: 0.8721 (tppp) cc_final: 0.8377 (mmtt) REVERT: D 600 ARG cc_start: 0.7401 (mtm110) cc_final: 0.6750 (mmm160) outliers start: 12 outliers final: 11 residues processed: 126 average time/residue: 0.7209 time to fit residues: 129.0180 Evaluate side-chains 130 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN C 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094815 restraints weight = 68132.517| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.15 r_work: 0.3005 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16352 Z= 0.175 Angle : 0.461 4.245 22380 Z= 0.259 Chirality : 0.039 0.142 2503 Planarity : 0.004 0.046 2710 Dihedral : 16.334 139.942 2752 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 0.84 % Allowed : 7.74 % Favored : 91.42 % 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: 0.62 (0.20), residues: 1824 helix: 2.58 (0.18), residues: 830 sheet: -0.59 (0.38), residues: 180 loop : -1.79 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS D 643 PHE 0.007 0.001 PHE C 368 TYR 0.009 0.001 TYR C 266 ARG 0.002 0.000 ARG B 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6239.71 seconds wall clock time: 110 minutes 17.00 seconds (6617.00 seconds total)