Starting phenix.real_space_refine on Thu Feb 15 16:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxo_24074/02_2024/7mxo_24074.pdb" } resolution = 3.47 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= 0.025 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 80 5.16 5 Cl 2 4.86 5 C 8370 2.51 5 N 2111 2.21 5 O 2267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6443 Classifications: {'peptide': 825} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 795} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 6385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6385 Classifications: {'peptide': 819} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 789} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.37, per 1000 atoms: 0.57 Number of scatterers: 12832 At special positions: 0 Unit cell: (112.32, 88.56, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 80 16.00 O 2267 8.00 N 2111 7.00 C 8370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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: 5.03 Conformation dependent library (CDL) restraints added in 2.2 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 64.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 285 through 291 removed outlier: 4.263A pdb=" N LYS A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.785A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.752A pdb=" N VAL A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 454 removed outlier: 3.562A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.552A pdb=" N GLY A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 Proline residue: A 519 - end of helix removed outlier: 3.876A pdb=" N LEU A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 4.331A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 575 through 580' Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.676A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 633 removed outlier: 3.708A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 639 through 643 Processing helix chain 'A' and resid 653 through 667 removed outlier: 3.801A pdb=" N LEU A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 699 Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.599A pdb=" N ILE A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 751 Processing helix chain 'A' and resid 763 through 780 removed outlier: 4.303A pdb=" N TYR A 767 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.000A pdb=" N LEU A 805 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 removed outlier: 3.539A pdb=" N GLU A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 873 Processing helix chain 'A' and resid 896 through 914 removed outlier: 3.665A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.687A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1050 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1135 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.336A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.905A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.579A pdb=" N VAL B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.271A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.074A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 544 removed outlier: 3.834A pdb=" N ILE B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Proline residue: B 519 - end of helix removed outlier: 3.586A pdb=" N LEU B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 580 removed outlier: 4.048A pdb=" N CYS B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.591A pdb=" N MET B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 633 removed outlier: 3.525A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 652 through 667 Processing helix chain 'B' and resid 674 through 699 removed outlier: 3.552A pdb=" N ILE B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 731 through 752 Processing helix chain 'B' and resid 762 through 780 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.898A pdb=" N LEU B 805 " --> pdb=" O ARG B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 4.269A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 849 " --> pdb=" O TRP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 873 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.840A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1046 Proline residue: B1040 - end of helix removed outlier: 3.962A pdb=" N LYS B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1090 through 1094 removed outlier: 4.402A pdb=" N ASN B1093 " --> pdb=" O GLY B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1109 removed outlier: 3.591A pdb=" N ILE B1101 " --> pdb=" O LYS B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1119 through 1128 removed outlier: 3.710A pdb=" N LYS B1125 " --> pdb=" O ASP B1121 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET B1126 " --> pdb=" O ILE B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing sheet with id=AA1, first strand: chain 'A' and resid 817 through 819 removed outlier: 6.398A pdb=" N GLN A 790 " --> pdb=" O THR A 883 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 885 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 792 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY A 887 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N MET A 794 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 920 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET A1087 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819 removed outlier: 6.375A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 920 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 761 hydrogen bonds defined for protein. 2247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 5.44 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: 4003 1.34 - 1.46: 1933 1.46 - 1.57: 7039 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 13111 Sorted by residual: bond pdb=" CG1 ILE A 415 " pdb=" CD1 ILE A 415 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG ARG B 844 " pdb=" CD ARG B 844 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CG LEU A 586 " pdb=" CD2 LEU A 586 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CB MET B 296 " pdb=" CG MET B 296 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ILE B 603 " pdb=" CG2 ILE B 603 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.94e-01 ... (remaining 13106 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.10: 200 105.10 - 112.34: 6837 112.34 - 119.58: 4380 119.58 - 126.82: 6176 126.82 - 134.06: 179 Bond angle restraints: 17772 Sorted by residual: angle pdb=" C GLN B 843 " pdb=" N ARG B 844 " pdb=" CA ARG B 844 " ideal model delta sigma weight residual 121.14 115.43 5.71 1.75e+00 3.27e-01 1.07e+01 angle pdb=" N GLU A1106 " pdb=" CA GLU A1106 " pdb=" CB GLU A1106 " ideal model delta sigma weight residual 110.28 114.20 -3.92 1.55e+00 4.16e-01 6.38e+00 angle pdb=" CA ARG B 844 " pdb=" CB ARG B 844 " pdb=" CG ARG B 844 " ideal model delta sigma weight residual 114.10 119.13 -5.03 2.00e+00 2.50e-01 6.34e+00 angle pdb=" N MET B 835 " pdb=" CA MET B 835 " pdb=" CB MET B 835 " ideal model delta sigma weight residual 110.28 114.13 -3.85 1.55e+00 4.16e-01 6.18e+00 angle pdb=" CB MET B 835 " pdb=" CG MET B 835 " pdb=" SD MET B 835 " ideal model delta sigma weight residual 112.70 120.15 -7.45 3.00e+00 1.11e-01 6.16e+00 ... (remaining 17767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6925 17.37 - 34.75: 711 34.75 - 52.12: 104 52.12 - 69.50: 13 69.50 - 86.87: 8 Dihedral angle restraints: 7761 sinusoidal: 3024 harmonic: 4737 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 54.48 38.52 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA PRO B 754 " pdb=" C PRO B 754 " pdb=" N ASP B 755 " pdb=" CA ASP B 755 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 7758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 493 0.068 - 0.102: 151 0.102 - 0.136: 55 0.136 - 0.170: 3 Chirality restraints: 2059 Sorted by residual: chirality pdb=" CA ILE A 730 " pdb=" N ILE A 730 " pdb=" C ILE A 730 " pdb=" CB ILE A 730 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA ILE B 668 " pdb=" N ILE B 668 " pdb=" C ILE B 668 " pdb=" CB ILE B 668 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE A 668 " pdb=" N ILE A 668 " pdb=" C ILE A 668 " pdb=" CB ILE A 668 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2056 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 801 " 0.240 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG A 801 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 801 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 801 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 801 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1102 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C ILE B1102 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE B1102 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B1103 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 495 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 496 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " 0.021 5.00e-02 4.00e+02 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 334 2.70 - 3.31: 15948 3.31 - 3.92: 24452 3.92 - 4.53: 32872 4.53 - 5.14: 50920 Nonbonded interactions: 124526 Sorted by model distance: nonbonded pdb=" OG1 THR B1094 " pdb=" NH1 ARG B1151 " model vdw 2.086 2.520 nonbonded pdb=" O GLY B 313 " pdb=" NH1 ARG B 546 " model vdw 2.088 2.520 nonbonded pdb=" O GLY A 313 " pdb=" NH1 ARG A 546 " model vdw 2.118 2.520 nonbonded pdb=" O ASP B1091 " pdb=" NH1 ARG B1151 " model vdw 2.133 2.520 nonbonded pdb=" OG1 THR B 328 " pdb=" OG1 THR B 530 " model vdw 2.144 2.440 ... (remaining 124521 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' and (resid 284 through 644 or resid 651 through 836 or (resid 837 and \ (name N or name CA or name C or name O or name CB )) or resid 838 through 922 o \ r resid 1020 through 1079 or resid 1081 through 1206 or resid 1301 through 1302) \ ) selection = chain 'B' } 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: 2.510 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: 10.290 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 36.850 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.053 13111 Z= 0.285 Angle : 0.584 7.448 17772 Z= 0.319 Chirality : 0.041 0.170 2059 Planarity : 0.004 0.107 2207 Dihedral : 13.623 86.874 4707 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 0.60 (0.21), residues: 1630 helix: 1.53 (0.17), residues: 973 sheet: -0.00 (0.52), residues: 110 loop : -1.65 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 287 HIS 0.004 0.001 HIS A 809 PHE 0.024 0.002 PHE A 907 TYR 0.023 0.002 TYR B 915 ARG 0.005 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.8597 (tp) cc_final: 0.8394 (tp) REVERT: A 852 LYS cc_start: 0.7570 (mptt) cc_final: 0.7150 (mptt) REVERT: A 902 MET cc_start: 0.7534 (ttp) cc_final: 0.7071 (ttm) REVERT: A 1205 GLN cc_start: 0.7462 (tm-30) cc_final: 0.7117 (tm-30) REVERT: B 354 TYR cc_start: 0.7125 (t80) cc_final: 0.6898 (t80) REVERT: B 433 LYS cc_start: 0.7802 (tptp) cc_final: 0.7146 (pptt) REVERT: B 818 MET cc_start: 0.7821 (tmm) cc_final: 0.7328 (tmm) REVERT: B 835 MET cc_start: 0.7882 (mpp) cc_final: 0.7599 (mtm) REVERT: B 903 TYR cc_start: 0.7734 (m-80) cc_final: 0.7094 (m-80) REVERT: B 1112 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6916 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2611 time to fit residues: 69.3192 Evaluate side-chains 156 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 77 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B1149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13111 Z= 0.218 Angle : 0.551 6.459 17772 Z= 0.291 Chirality : 0.042 0.150 2059 Planarity : 0.004 0.042 2207 Dihedral : 4.308 19.092 1748 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.58 % Allowed : 9.43 % Favored : 89.99 % 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: 0.84 (0.21), residues: 1630 helix: 1.69 (0.17), residues: 979 sheet: 0.37 (0.52), residues: 99 loop : -1.54 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 892 HIS 0.002 0.001 HIS A 824 PHE 0.024 0.001 PHE A 387 TYR 0.009 0.001 TYR B 353 ARG 0.004 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 1.380 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 402 MET cc_start: 0.7328 (tpp) cc_final: 0.7013 (tpp) REVERT: A 852 LYS cc_start: 0.7598 (mptt) cc_final: 0.7202 (mptt) REVERT: A 902 MET cc_start: 0.7481 (ttp) cc_final: 0.6913 (ttm) REVERT: A 1205 GLN cc_start: 0.7293 (tm-30) cc_final: 0.7087 (tm-30) REVERT: B 354 TYR cc_start: 0.7136 (t80) cc_final: 0.6881 (t80) REVERT: B 433 LYS cc_start: 0.7806 (tptp) cc_final: 0.7186 (pptt) REVERT: B 632 ASP cc_start: 0.7641 (t0) cc_final: 0.7389 (t0) REVERT: B 818 MET cc_start: 0.7971 (tmm) cc_final: 0.7321 (tmm) REVERT: B 835 MET cc_start: 0.7496 (mpp) cc_final: 0.7038 (mpp) REVERT: B 843 GLN cc_start: 0.8423 (tt0) cc_final: 0.8129 (tt0) REVERT: B 1186 TRP cc_start: 0.8755 (m-10) cc_final: 0.8524 (m-10) outliers start: 8 outliers final: 4 residues processed: 181 average time/residue: 0.2487 time to fit residues: 65.5028 Evaluate side-chains 159 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 597 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS A1137 ASN ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 763 GLN B 908 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13111 Z= 0.284 Angle : 0.581 8.504 17772 Z= 0.305 Chirality : 0.043 0.159 2059 Planarity : 0.004 0.046 2207 Dihedral : 4.325 19.622 1748 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.23 % Allowed : 13.13 % Favored : 85.64 % 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: 0.71 (0.21), residues: 1630 helix: 1.58 (0.16), residues: 979 sheet: 0.00 (0.50), residues: 114 loop : -1.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 892 HIS 0.005 0.001 HIS A 398 PHE 0.023 0.002 PHE B 811 TYR 0.008 0.001 TYR A 353 ARG 0.004 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.7385 (tpp) cc_final: 0.6590 (tpt) REVERT: A 775 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9247 (mm) REVERT: A 852 LYS cc_start: 0.7632 (mptt) cc_final: 0.7207 (mptt) REVERT: A 902 MET cc_start: 0.7410 (ttp) cc_final: 0.6805 (ttm) REVERT: A 1205 GLN cc_start: 0.7300 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 354 TYR cc_start: 0.7196 (t80) cc_final: 0.6902 (t80) REVERT: B 402 MET cc_start: 0.6437 (ptp) cc_final: 0.5917 (ptp) REVERT: B 433 LYS cc_start: 0.7831 (tptp) cc_final: 0.7204 (pptt) REVERT: B 632 ASP cc_start: 0.7666 (t0) cc_final: 0.7417 (t0) REVERT: B 718 LEU cc_start: 0.8227 (mp) cc_final: 0.7817 (tt) REVERT: B 818 MET cc_start: 0.8132 (tmm) cc_final: 0.7509 (tmm) REVERT: B 835 MET cc_start: 0.7452 (mpp) cc_final: 0.6893 (mtt) REVERT: B 844 ARG cc_start: 0.8767 (pmt-80) cc_final: 0.8359 (pmt-80) REVERT: B 903 TYR cc_start: 0.7873 (m-80) cc_final: 0.7451 (m-80) outliers start: 17 outliers final: 8 residues processed: 186 average time/residue: 0.2522 time to fit residues: 67.8197 Evaluate side-chains 168 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 697 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 0.0870 chunk 157 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13111 Z= 0.190 Angle : 0.526 8.251 17772 Z= 0.274 Chirality : 0.041 0.152 2059 Planarity : 0.003 0.044 2207 Dihedral : 4.206 19.340 1748 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.52 % Allowed : 14.79 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1630 helix: 1.70 (0.17), residues: 984 sheet: 0.04 (0.50), residues: 114 loop : -1.61 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 892 HIS 0.005 0.001 HIS B 908 PHE 0.023 0.001 PHE B 811 TYR 0.008 0.001 TYR A 354 ARG 0.002 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.457 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 666 ILE cc_start: 0.8373 (pt) cc_final: 0.8045 (mt) REVERT: A 852 LYS cc_start: 0.7668 (mptt) cc_final: 0.7235 (mptt) REVERT: A 902 MET cc_start: 0.7356 (ttp) cc_final: 0.6679 (ttm) REVERT: A 1205 GLN cc_start: 0.7303 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 354 TYR cc_start: 0.7214 (t80) cc_final: 0.6938 (t80) REVERT: B 382 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8215 (ttm) REVERT: B 433 LYS cc_start: 0.7760 (tptp) cc_final: 0.7194 (pptt) REVERT: B 632 ASP cc_start: 0.7616 (t0) cc_final: 0.7352 (t0) REVERT: B 718 LEU cc_start: 0.8155 (mp) cc_final: 0.7753 (tt) REVERT: B 818 MET cc_start: 0.8195 (tmm) cc_final: 0.7628 (ttp) REVERT: B 835 MET cc_start: 0.7517 (mpp) cc_final: 0.7211 (mtp) REVERT: B 843 GLN cc_start: 0.8228 (tt0) cc_final: 0.7927 (tt0) REVERT: B 903 TYR cc_start: 0.7818 (m-80) cc_final: 0.7384 (m-80) REVERT: B 1186 TRP cc_start: 0.8777 (m-10) cc_final: 0.8507 (m-10) outliers start: 21 outliers final: 12 residues processed: 183 average time/residue: 0.2694 time to fit residues: 72.0027 Evaluate side-chains 167 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13111 Z= 0.215 Angle : 0.545 9.944 17772 Z= 0.284 Chirality : 0.041 0.158 2059 Planarity : 0.003 0.044 2207 Dihedral : 4.178 19.546 1748 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 15.95 % Favored : 82.16 % 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: 0.82 (0.21), residues: 1630 helix: 1.70 (0.16), residues: 985 sheet: 0.06 (0.49), residues: 114 loop : -1.61 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 892 HIS 0.003 0.001 HIS A 824 PHE 0.023 0.001 PHE B 811 TYR 0.011 0.001 TYR B 767 ARG 0.003 0.000 ARG B 844 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.517 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 666 ILE cc_start: 0.8368 (pt) cc_final: 0.8022 (mt) REVERT: A 852 LYS cc_start: 0.7679 (mptt) cc_final: 0.7291 (mptt) REVERT: A 902 MET cc_start: 0.7350 (ttp) cc_final: 0.6862 (ttm) REVERT: B 354 TYR cc_start: 0.7186 (t80) cc_final: 0.6935 (t80) REVERT: B 433 LYS cc_start: 0.7802 (tptp) cc_final: 0.7267 (pptt) REVERT: B 632 ASP cc_start: 0.7635 (t0) cc_final: 0.7364 (t0) REVERT: B 718 LEU cc_start: 0.8169 (mp) cc_final: 0.7740 (tt) REVERT: B 833 LYS cc_start: 0.7864 (mttt) cc_final: 0.7636 (mtmt) REVERT: B 834 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7458 (pt0) REVERT: B 843 GLN cc_start: 0.8245 (tt0) cc_final: 0.7920 (tt0) REVERT: B 844 ARG cc_start: 0.8749 (pmt-80) cc_final: 0.8519 (pmt-80) REVERT: B 903 TYR cc_start: 0.7792 (m-80) cc_final: 0.6817 (t80) REVERT: B 914 GLN cc_start: 0.7712 (pp30) cc_final: 0.7267 (mm-40) REVERT: B 1186 TRP cc_start: 0.8808 (m-10) cc_final: 0.8534 (m-10) outliers start: 26 outliers final: 21 residues processed: 185 average time/residue: 0.2529 time to fit residues: 67.8016 Evaluate side-chains 179 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13111 Z= 0.288 Angle : 0.589 8.906 17772 Z= 0.309 Chirality : 0.043 0.168 2059 Planarity : 0.004 0.050 2207 Dihedral : 4.306 23.673 1748 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.10 % Allowed : 16.90 % Favored : 81.00 % 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 (0.21), residues: 1630 helix: 1.51 (0.16), residues: 993 sheet: 0.08 (0.50), residues: 114 loop : -1.68 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 892 HIS 0.003 0.001 HIS A 824 PHE 0.023 0.002 PHE B 811 TYR 0.008 0.001 TYR A1183 ARG 0.003 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.438 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 775 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9284 (mm) REVERT: A 825 MET cc_start: 0.7809 (mmm) cc_final: 0.7600 (mmm) REVERT: A 852 LYS cc_start: 0.7724 (mptt) cc_final: 0.7364 (mptt) REVERT: A 902 MET cc_start: 0.7366 (ttp) cc_final: 0.6825 (ttm) REVERT: B 354 TYR cc_start: 0.7189 (t80) cc_final: 0.6921 (t80) REVERT: B 433 LYS cc_start: 0.7799 (tptp) cc_final: 0.7286 (pptt) REVERT: B 818 MET cc_start: 0.8214 (tmm) cc_final: 0.7351 (tmm) REVERT: B 834 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7529 (pt0) REVERT: B 844 ARG cc_start: 0.8865 (pmt-80) cc_final: 0.8488 (pmt-80) REVERT: B 903 TYR cc_start: 0.7820 (m-80) cc_final: 0.6767 (t80) REVERT: B 1186 TRP cc_start: 0.8813 (m-10) cc_final: 0.8551 (m-10) outliers start: 29 outliers final: 25 residues processed: 174 average time/residue: 0.2614 time to fit residues: 67.2630 Evaluate side-chains 176 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 4.9990 chunk 17 optimal weight: 0.0010 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN A 824 HIS ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13111 Z= 0.199 Angle : 0.551 10.734 17772 Z= 0.288 Chirality : 0.041 0.174 2059 Planarity : 0.003 0.043 2207 Dihedral : 4.246 34.593 1748 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.89 % Allowed : 17.84 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.77 (0.21), residues: 1630 helix: 1.64 (0.17), residues: 995 sheet: 0.09 (0.50), residues: 114 loop : -1.65 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 892 HIS 0.002 0.000 HIS A 824 PHE 0.024 0.001 PHE B 811 TYR 0.010 0.001 TYR A 354 ARG 0.001 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.452 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 587 MET cc_start: 0.7672 (tpp) cc_final: 0.7329 (tpp) REVERT: A 666 ILE cc_start: 0.8360 (pt) cc_final: 0.8043 (mt) REVERT: A 788 ARG cc_start: 0.7475 (mpt180) cc_final: 0.7135 (mpt180) REVERT: A 852 LYS cc_start: 0.7624 (mptt) cc_final: 0.7274 (mptt) REVERT: A 902 MET cc_start: 0.7346 (ttp) cc_final: 0.6736 (ttm) REVERT: B 433 LYS cc_start: 0.7839 (tptp) cc_final: 0.7345 (pptt) REVERT: B 818 MET cc_start: 0.8253 (tmm) cc_final: 0.7300 (tmm) REVERT: B 871 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7546 (mtp) REVERT: B 903 TYR cc_start: 0.7938 (m-80) cc_final: 0.6794 (t80) REVERT: B 914 GLN cc_start: 0.7545 (pp30) cc_final: 0.6979 (mm-40) REVERT: B 1186 TRP cc_start: 0.8817 (m-10) cc_final: 0.8569 (m-10) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.2813 time to fit residues: 72.6464 Evaluate side-chains 172 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 107 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 123 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13111 Z= 0.189 Angle : 0.561 10.608 17772 Z= 0.289 Chirality : 0.041 0.182 2059 Planarity : 0.003 0.043 2207 Dihedral : 4.215 38.026 1748 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.81 % Allowed : 18.49 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.86 (0.21), residues: 1630 helix: 1.71 (0.17), residues: 991 sheet: 0.15 (0.50), residues: 115 loop : -1.62 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 892 HIS 0.003 0.000 HIS A 806 PHE 0.025 0.001 PHE B 811 TYR 0.010 0.001 TYR A 354 ARG 0.003 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.447 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 408 ASP cc_start: 0.7643 (m-30) cc_final: 0.7386 (m-30) REVERT: A 587 MET cc_start: 0.7681 (tpp) cc_final: 0.7331 (tpp) REVERT: A 641 PHE cc_start: 0.6974 (m-80) cc_final: 0.6248 (m-80) REVERT: A 666 ILE cc_start: 0.8361 (pt) cc_final: 0.8042 (mt) REVERT: A 852 LYS cc_start: 0.7666 (mptt) cc_final: 0.7325 (mptt) REVERT: A 902 MET cc_start: 0.7335 (ttp) cc_final: 0.6691 (ttm) REVERT: B 354 TYR cc_start: 0.7224 (t80) cc_final: 0.6952 (t80) REVERT: B 433 LYS cc_start: 0.7829 (tptp) cc_final: 0.7336 (pptt) REVERT: B 818 MET cc_start: 0.8225 (tmm) cc_final: 0.7330 (tmm) REVERT: B 843 GLN cc_start: 0.8351 (tt0) cc_final: 0.8057 (tt0) REVERT: B 871 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7528 (mtp) REVERT: B 903 TYR cc_start: 0.7892 (m-80) cc_final: 0.6786 (t80) REVERT: B 914 GLN cc_start: 0.7730 (pp30) cc_final: 0.7341 (mm-40) REVERT: B 1186 TRP cc_start: 0.8798 (m-10) cc_final: 0.8551 (m-10) outliers start: 25 outliers final: 22 residues processed: 182 average time/residue: 0.2605 time to fit residues: 69.4001 Evaluate side-chains 180 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1135 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 859 HIS ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13111 Z= 0.373 Angle : 0.643 9.548 17772 Z= 0.334 Chirality : 0.044 0.185 2059 Planarity : 0.004 0.041 2207 Dihedral : 4.477 37.948 1748 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.32 % Allowed : 18.35 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.50 (0.21), residues: 1630 helix: 1.40 (0.16), residues: 988 sheet: 0.42 (0.52), residues: 106 loop : -1.78 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 892 HIS 0.003 0.001 HIS B 908 PHE 0.025 0.002 PHE B 811 TYR 0.011 0.002 TYR A 739 ARG 0.003 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.7767 (tpp) cc_final: 0.7424 (tpp) REVERT: A 851 MET cc_start: 0.5912 (mmp) cc_final: 0.4733 (mtm) REVERT: A 852 LYS cc_start: 0.7665 (mptt) cc_final: 0.7249 (mttt) REVERT: A 902 MET cc_start: 0.7366 (ttp) cc_final: 0.6769 (ttm) REVERT: A 1097 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8094 (mtmm) REVERT: B 433 LYS cc_start: 0.7839 (tptp) cc_final: 0.7450 (pptt) REVERT: B 818 MET cc_start: 0.8182 (tmm) cc_final: 0.7359 (tmm) REVERT: B 835 MET cc_start: 0.7327 (mpp) cc_final: 0.6990 (mpp) REVERT: B 903 TYR cc_start: 0.7935 (m-80) cc_final: 0.6755 (t80) REVERT: B 914 GLN cc_start: 0.7699 (pp30) cc_final: 0.7213 (mm-40) REVERT: B 1066 ASP cc_start: 0.8303 (m-30) cc_final: 0.8090 (t0) REVERT: B 1106 GLU cc_start: 0.8881 (mp0) cc_final: 0.8606 (pt0) REVERT: B 1186 TRP cc_start: 0.8847 (m-10) cc_final: 0.8547 (m-10) outliers start: 32 outliers final: 27 residues processed: 183 average time/residue: 0.2466 time to fit residues: 66.1842 Evaluate side-chains 180 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1135 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13111 Z= 0.226 Angle : 0.593 9.941 17772 Z= 0.306 Chirality : 0.042 0.191 2059 Planarity : 0.003 0.042 2207 Dihedral : 4.348 38.686 1748 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.25 % Allowed : 18.56 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.66 (0.21), residues: 1630 helix: 1.56 (0.17), residues: 990 sheet: 0.22 (0.50), residues: 115 loop : -1.74 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 892 HIS 0.002 0.000 HIS A 859 PHE 0.025 0.001 PHE B 811 TYR 0.012 0.001 TYR A 353 ARG 0.003 0.000 ARG A 801 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.314 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 587 MET cc_start: 0.7732 (tpp) cc_final: 0.7400 (tpp) REVERT: A 851 MET cc_start: 0.6128 (mmp) cc_final: 0.4908 (mtm) REVERT: A 852 LYS cc_start: 0.7655 (mptt) cc_final: 0.7248 (mttt) REVERT: A 902 MET cc_start: 0.7385 (ttp) cc_final: 0.6720 (ttm) REVERT: A 1097 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: B 818 MET cc_start: 0.8146 (tmm) cc_final: 0.7150 (tmm) REVERT: B 835 MET cc_start: 0.7308 (mpp) cc_final: 0.6906 (mpp) REVERT: B 871 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7576 (mtp) REVERT: B 903 TYR cc_start: 0.7999 (m-80) cc_final: 0.6768 (t80) REVERT: B 914 GLN cc_start: 0.7647 (pp30) cc_final: 0.7250 (mm-40) REVERT: B 1186 TRP cc_start: 0.8802 (m-10) cc_final: 0.8571 (m-10) outliers start: 31 outliers final: 28 residues processed: 181 average time/residue: 0.2451 time to fit residues: 64.6794 Evaluate side-chains 182 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1135 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.202662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136025 restraints weight = 16575.613| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.35 r_work: 0.3399 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13111 Z= 0.182 Angle : 0.561 9.630 17772 Z= 0.291 Chirality : 0.041 0.213 2059 Planarity : 0.003 0.043 2207 Dihedral : 4.211 39.864 1748 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.89 % Allowed : 19.36 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.79 (0.21), residues: 1630 helix: 1.69 (0.17), residues: 996 sheet: 0.26 (0.50), residues: 115 loop : -1.79 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 892 HIS 0.002 0.000 HIS A 859 PHE 0.034 0.001 PHE A 708 TYR 0.010 0.001 TYR A 353 ARG 0.002 0.000 ARG A 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.27 seconds wall clock time: 54 minutes 0.74 seconds (3240.74 seconds total)