Starting phenix.real_space_refine on Fri Feb 16 22:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crw_30458/02_2024/7crw_30458.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 10687 2.51 5 N 2832 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 41": "NH1" <-> "NH2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A GLU 1076": "OE1" <-> "OE2" Residue "A TYR 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1101": "OE1" <-> "OE2" Residue "B ARG 976": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 774": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16613 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 6765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6765 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 53, 'TRANS': 783} Chain breaks: 1 Chain: "A" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2225 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 258} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1096 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "C" Number of atoms: 6527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6527 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 53, 'TRANS': 753} Chain breaks: 5 Time building chain proxies: 9.14, per 1000 atoms: 0.55 Number of scatterers: 16613 At special positions: 0 Unit cell: (103.978, 149.601, 113.527, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 3015 8.00 N 2832 7.00 C 10687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 3.0 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 35 sheets defined 18.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.500A pdb=" N GLY D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 391 through 402 removed outlier: 3.548A pdb=" N GLU D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 400 " --> pdb=" O GLN D 396 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 670 Processing helix chain 'D' and resid 685 through 690 removed outlier: 3.765A pdb=" N GLU D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 715 removed outlier: 3.785A pdb=" N ASP D 703 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 711 " --> pdb=" O GLY D 707 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 742 Processing helix chain 'D' and resid 757 through 761 removed outlier: 3.818A pdb=" N ALA D 760 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 761 " --> pdb=" O TRP D 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 757 through 761' Processing helix chain 'D' and resid 762 through 771 removed outlier: 4.623A pdb=" N ARG D 768 " --> pdb=" O GLY D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 784 removed outlier: 3.557A pdb=" N ASN D 776 " --> pdb=" O VAL D 772 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN D 778 " --> pdb=" O GLU D 774 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY D 779 " --> pdb=" O ASN D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 4.098A pdb=" N VAL D 789 " --> pdb=" O ALA D 786 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU D 790 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 824 Processing helix chain 'D' and resid 843 through 862 Processing helix chain 'A' and resid 887 through 893 removed outlier: 4.166A pdb=" N PHE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 900 removed outlier: 3.655A pdb=" N HIS A 899 " --> pdb=" O PRO A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 1012 through 1025 Processing helix chain 'B' and resid 1013 through 1025 removed outlier: 3.609A pdb=" N LYS B1017 " --> pdb=" O CYS B1013 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B1021 " --> pdb=" O LYS B1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.573A pdb=" N GLN C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 670 removed outlier: 3.747A pdb=" N GLY C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 692 removed outlier: 3.684A pdb=" N LEU C 692 " --> pdb=" O GLU C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 removed outlier: 3.601A pdb=" N ASP C 703 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 742 Processing helix chain 'C' and resid 757 through 761 removed outlier: 3.802A pdb=" N ALA C 760 " --> pdb=" O VAL C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 4.218A pdb=" N ARG C 768 " --> pdb=" O GLY C 764 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 769 " --> pdb=" O TYR C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 775 Processing helix chain 'C' and resid 776 through 782 removed outlier: 4.131A pdb=" N GLU C 781 " --> pdb=" O GLN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 4.540A pdb=" N VAL C 789 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU C 790 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 825 removed outlier: 3.923A pdb=" N ARG C 824 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.747A pdb=" N THR C 853 " --> pdb=" O HIS C 849 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.726A pdb=" N HIS D 69 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.546A pdb=" N LEU D 99 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'D' and resid 188 through 192 removed outlier: 6.503A pdb=" N SER D 201 " --> pdb=" O PRO D 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE D 192 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 199 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 236 through 238 Processing sheet with id=AA6, first strand: chain 'D' and resid 236 through 238 Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 272 removed outlier: 6.532A pdb=" N GLN D 322 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 286 through 290 Processing sheet with id=AA9, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'D' and resid 350 through 356 removed outlier: 5.738A pdb=" N ILE D 351 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU D 368 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D 353 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 375 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D 413 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 377 " --> pdb=" O ILE D 411 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 426 through 428 removed outlier: 6.518A pdb=" N ASP D 459 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 482 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AB4, first strand: chain 'D' and resid 546 through 551 removed outlier: 3.513A pdb=" N SER D 563 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER D 564 " --> pdb=" O PRO D 568 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 571 " --> pdb=" O MET D 594 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS D 575 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE D 590 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER D 577 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 613 removed outlier: 4.561A pdb=" N TYR D 621 " --> pdb=" O ASP D 677 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 677 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 673 " --> pdb=" O TYR D 625 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL D 674 " --> pdb=" O PRO D 637 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 639 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE D 676 " --> pdb=" O VAL D 639 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 641 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS D 636 " --> pdb=" O ASP D 719 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER D 721 " --> pdb=" O HIS D 636 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR D 638 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL D 723 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU D 640 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE D 725 " --> pdb=" O LEU D 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 750 through 752 removed outlier: 6.379A pdb=" N ILE D 801 " --> pdb=" O GLN D 832 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR D 834 " --> pdb=" O ILE D 801 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS D 803 " --> pdb=" O TYR D 834 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 845 through 848 removed outlier: 4.194A pdb=" N GLU A 845 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 853 " --> pdb=" O VAL A 847 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 862 through 866 removed outlier: 4.052A pdb=" N ARG A 955 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 986 through 987 removed outlier: 3.518A pdb=" N LEU A1040 " --> pdb=" O ILE A 987 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1029 through 1031 removed outlier: 4.163A pdb=" N ILE A 993 " --> pdb=" O ILE A1031 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1055 " --> pdb=" O TYR A1078 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1060 through 1062 removed outlier: 3.707A pdb=" N TRP A1100 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A1092 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A1098 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1029 through 1031 removed outlier: 4.133A pdb=" N ILE B 993 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1060 through 1062 Processing sheet with id=AC5, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.812A pdb=" N ILE C 90 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG C 70 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER C 88 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR C 72 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 86 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 74 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 84 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 142 through 144 Processing sheet with id=AC7, first strand: chain 'C' and resid 188 through 193 removed outlier: 6.575A pdb=" N SER C 201 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE C 192 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE C 199 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AC9, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AD1, first strand: chain 'C' and resid 270 through 272 removed outlier: 6.551A pdb=" N GLN C 322 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 286 through 290 Processing sheet with id=AD3, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AD4, first strand: chain 'C' and resid 350 through 356 removed outlier: 5.459A pdb=" N ILE C 351 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 368 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 353 " --> pdb=" O MET C 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 426 through 428 removed outlier: 6.759A pdb=" N ARG C 455 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU C 485 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 457 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AD7, first strand: chain 'C' and resid 546 through 551 removed outlier: 3.643A pdb=" N HIS C 561 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 559 " --> pdb=" O SER C 550 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER C 564 " --> pdb=" O PRO C 568 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 571 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER C 593 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 573 " --> pdb=" O TRP C 591 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 587 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 608 through 613 removed outlier: 4.175A pdb=" N TYR C 621 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 673 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL C 674 " --> pdb=" O PRO C 637 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 639 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 676 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE C 641 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS C 636 " --> pdb=" O ASP C 719 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER C 721 " --> pdb=" O HIS C 636 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR C 638 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 723 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 640 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 725 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ILE C 750 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 725 " --> pdb=" O ILE C 750 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY C 752 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 727 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA C 749 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU C 802 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 751 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY C 804 " --> pdb=" O ALA C 751 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLN C 832 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 801 " --> pdb=" O GLN C 832 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR C 834 " --> pdb=" O ILE C 801 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS C 803 " --> pdb=" O TYR C 834 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1347 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: 6.58 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3858 1.33 - 1.45: 3786 1.45 - 1.57: 9339 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 17100 Sorted by residual: bond pdb=" N CYS C 600 " pdb=" CA CYS C 600 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.10e-03 1.21e+04 1.86e+01 bond pdb=" C THR C 567 " pdb=" N PRO C 568 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" N ILE A1082 " pdb=" CA ILE A1082 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.07e-02 8.73e+03 1.03e+01 bond pdb=" N ASP D 603 " pdb=" CA ASP D 603 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 9.95e+00 bond pdb=" C CYS C 600 " pdb=" O CYS C 600 " ideal model delta sigma weight residual 1.233 1.248 -0.015 4.80e-03 4.34e+04 9.61e+00 ... (remaining 17095 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.14: 566 106.14 - 113.20: 9066 113.20 - 120.26: 6293 120.26 - 127.32: 7025 127.32 - 134.38: 273 Bond angle restraints: 23223 Sorted by residual: angle pdb=" N PRO C 601 " pdb=" CA PRO C 601 " pdb=" C PRO C 601 " ideal model delta sigma weight residual 110.70 126.03 -15.33 1.22e+00 6.72e-01 1.58e+02 angle pdb=" N PRO D 601 " pdb=" CA PRO D 601 " pdb=" C PRO D 601 " ideal model delta sigma weight residual 110.70 125.22 -14.52 1.22e+00 6.72e-01 1.42e+02 angle pdb=" N ILE A1082 " pdb=" CA ILE A1082 " pdb=" C ILE A1082 " ideal model delta sigma weight residual 113.10 105.42 7.68 9.70e-01 1.06e+00 6.27e+01 angle pdb=" N PRO C 602 " pdb=" CA PRO C 602 " pdb=" C PRO C 602 " ideal model delta sigma weight residual 112.47 124.58 -12.11 2.06e+00 2.36e-01 3.46e+01 angle pdb=" N VAL A 981 " pdb=" CA VAL A 981 " pdb=" C VAL A 981 " ideal model delta sigma weight residual 113.71 108.53 5.18 9.50e-01 1.11e+00 2.97e+01 ... (remaining 23218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 9010 15.94 - 31.89: 901 31.89 - 47.83: 170 47.83 - 63.78: 39 63.78 - 79.72: 17 Dihedral angle restraints: 10137 sinusoidal: 4141 harmonic: 5996 Sorted by residual: dihedral pdb=" CA ALA C 154 " pdb=" C ALA C 154 " pdb=" N SER C 155 " pdb=" CA SER C 155 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA SER C 729 " pdb=" C SER C 729 " pdb=" N TYR C 730 " pdb=" CA TYR C 730 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA VAL C 772 " pdb=" C VAL C 772 " pdb=" N PRO C 773 " pdb=" CA PRO C 773 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 10134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2386 0.111 - 0.222: 69 0.222 - 0.334: 9 0.334 - 0.445: 2 0.445 - 0.556: 2 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA PRO C 601 " pdb=" N PRO C 601 " pdb=" C PRO C 601 " pdb=" CB PRO C 601 " both_signs ideal model delta sigma weight residual False 2.72 2.16 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" CA PRO D 601 " pdb=" N PRO D 601 " pdb=" C PRO D 601 " pdb=" CB PRO D 601 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA LEU A1057 " pdb=" N LEU A1057 " pdb=" C LEU A1057 " pdb=" CB LEU A1057 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2465 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 599 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C SER D 599 " 0.052 2.00e-02 2.50e+03 pdb=" O SER D 599 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS D 600 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1077 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ILE A1077 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A1077 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR A1078 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1056 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ILE A1056 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A1056 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A1057 " 0.016 2.00e-02 2.50e+03 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1593 2.74 - 3.28: 15985 3.28 - 3.82: 26760 3.82 - 4.36: 33296 4.36 - 4.90: 56843 Nonbonded interactions: 134477 Sorted by model distance: nonbonded pdb=" NH1 ARG D 251 " pdb=" O ILE D 351 " model vdw 2.202 2.520 nonbonded pdb=" NH1 ARG C 219 " pdb=" OG SER C 332 " model vdw 2.227 2.520 nonbonded pdb=" OG SER A 989 " pdb=" O VAL A1009 " model vdw 2.228 2.440 nonbonded pdb=" O ARG D 306 " pdb=" OG SER D 309 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR C 72 " pdb=" OD2 ASP C 163 " model vdw 2.249 2.440 ... (remaining 134472 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 'C' selection = (chain 'D' and (resid 21 through 44 or resid 50 through 62 or resid 65 through 1 \ 15 or resid 136 through 227 or resid 231 through 862)) } 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=0.38 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: 0.900 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: 0.020 Extract box with map and model: 3.930 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.080 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.005 0.042 17100 Z= 0.324 Angle : 0.732 15.334 23223 Z= 0.468 Chirality : 0.053 0.556 2468 Planarity : 0.004 0.038 3007 Dihedral : 13.491 79.722 6277 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 0.60 % Allowed : 5.16 % Favored : 94.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.16), residues: 2037 helix: -3.08 (0.20), residues: 319 sheet: -2.21 (0.19), residues: 636 loop : -2.39 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 419 HIS 0.006 0.001 HIS C 803 PHE 0.014 0.001 PHE A 960 TYR 0.014 0.002 TYR D 531 ARG 0.005 0.000 ARG C 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8371 (pp30) cc_final: 0.7946 (pp30) REVERT: A 948 MET cc_start: 0.8233 (ttp) cc_final: 0.7974 (ttt) REVERT: A 1046 TYR cc_start: 0.8501 (m-80) cc_final: 0.7784 (m-80) REVERT: A 1084 SER cc_start: 0.8745 (m) cc_final: 0.8476 (t) REVERT: A 1093 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8616 (ttmm) REVERT: C 188 MET cc_start: 0.7926 (mtp) cc_final: 0.7663 (mtm) REVERT: C 250 ASP cc_start: 0.7341 (t0) cc_final: 0.7101 (t0) outliers start: 11 outliers final: 2 residues processed: 185 average time/residue: 0.3449 time to fit residues: 92.0472 Evaluate side-chains 118 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain C residue 573 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 69 HIS D 117 HIS D 160 HIS D 204 ASN D 311 ASN D 506 ASN D 515 GLN D 547 HIS ** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 647 GLN D 649 GLN D 803 HIS ** D 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 836 ASN D 859 GLN A 852 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 311 ASN C 339 GLN C 506 ASN C 803 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17100 Z= 0.198 Angle : 0.588 15.466 23223 Z= 0.304 Chirality : 0.044 0.187 2468 Planarity : 0.004 0.042 3007 Dihedral : 5.182 49.582 2238 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 1.37 % Allowed : 9.77 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.17), residues: 2037 helix: -1.40 (0.26), residues: 322 sheet: -1.69 (0.19), residues: 633 loop : -1.94 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 395 HIS 0.005 0.001 HIS A 946 PHE 0.013 0.001 PHE C 688 TYR 0.020 0.002 TYR A 998 ARG 0.007 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.993 Fit side-chains REVERT: A 898 GLN cc_start: 0.8274 (pp30) cc_final: 0.7925 (pp30) REVERT: A 948 MET cc_start: 0.8153 (ttp) cc_final: 0.7894 (ttt) REVERT: A 1084 SER cc_start: 0.8835 (m) cc_final: 0.8590 (t) REVERT: C 188 MET cc_start: 0.7819 (mtp) cc_final: 0.7592 (mtm) REVERT: C 250 ASP cc_start: 0.7265 (t0) cc_final: 0.7036 (t0) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.3111 time to fit residues: 63.2407 Evaluate side-chains 125 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 748 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 184 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS B1072 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 GLN C 547 HIS C 839 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17100 Z= 0.256 Angle : 0.574 14.635 23223 Z= 0.296 Chirality : 0.044 0.187 2468 Planarity : 0.004 0.046 3007 Dihedral : 4.972 30.678 2236 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 1.81 % Allowed : 11.96 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2037 helix: -0.86 (0.28), residues: 323 sheet: -1.43 (0.20), residues: 643 loop : -1.70 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 257 HIS 0.005 0.001 HIS A 946 PHE 0.014 0.001 PHE C 688 TYR 0.021 0.002 TYR A1078 ARG 0.008 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8295 (pp30) cc_final: 0.7935 (pp30) REVERT: A 948 MET cc_start: 0.8140 (ttp) cc_final: 0.7857 (ttt) REVERT: A 1084 SER cc_start: 0.8795 (m) cc_final: 0.8551 (t) REVERT: C 250 ASP cc_start: 0.7345 (t0) cc_final: 0.7073 (t0) outliers start: 33 outliers final: 21 residues processed: 139 average time/residue: 0.2877 time to fit residues: 62.1376 Evaluate side-chains 134 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 196 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 339 GLN ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17100 Z= 0.180 Angle : 0.535 12.721 23223 Z= 0.275 Chirality : 0.043 0.188 2468 Planarity : 0.004 0.050 3007 Dihedral : 4.776 31.030 2236 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 2.03 % Allowed : 12.95 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.18), residues: 2037 helix: -0.43 (0.29), residues: 324 sheet: -1.15 (0.20), residues: 643 loop : -1.47 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 836 HIS 0.004 0.001 HIS A 946 PHE 0.012 0.001 PHE C 688 TYR 0.016 0.001 TYR A 998 ARG 0.006 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 2.000 Fit side-chains REVERT: D 379 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 898 GLN cc_start: 0.8279 (pp30) cc_final: 0.7915 (pp30) REVERT: A 1084 SER cc_start: 0.8730 (m) cc_final: 0.8478 (t) REVERT: C 250 ASP cc_start: 0.7133 (t0) cc_final: 0.6870 (t0) outliers start: 37 outliers final: 25 residues processed: 152 average time/residue: 0.2871 time to fit residues: 67.1672 Evaluate side-chains 139 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 611 HIS D 704 GLN ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17100 Z= 0.401 Angle : 0.622 14.270 23223 Z= 0.319 Chirality : 0.046 0.187 2468 Planarity : 0.005 0.054 3007 Dihedral : 5.040 30.202 2236 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 2.20 % Allowed : 14.82 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 2037 helix: -0.42 (0.28), residues: 325 sheet: -1.20 (0.20), residues: 656 loop : -1.44 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 504 HIS 0.006 0.001 HIS D 726 PHE 0.017 0.002 PHE C 688 TYR 0.021 0.002 TYR B1046 ARG 0.010 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 2.173 Fit side-chains REVERT: A 898 GLN cc_start: 0.8345 (pp30) cc_final: 0.7942 (pp30) REVERT: A 1084 SER cc_start: 0.8756 (m) cc_final: 0.8496 (t) REVERT: B 1020 ASP cc_start: 0.8324 (t0) cc_final: 0.7982 (m-30) REVERT: C 250 ASP cc_start: 0.7337 (t0) cc_final: 0.7075 (t0) outliers start: 40 outliers final: 30 residues processed: 148 average time/residue: 0.2937 time to fit residues: 67.3777 Evaluate side-chains 149 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17100 Z= 0.184 Angle : 0.548 15.751 23223 Z= 0.281 Chirality : 0.044 0.188 2468 Planarity : 0.004 0.055 3007 Dihedral : 4.828 31.068 2236 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 2.74 % Allowed : 15.15 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2037 helix: -0.12 (0.29), residues: 325 sheet: -0.97 (0.20), residues: 650 loop : -1.33 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 257 HIS 0.004 0.001 HIS C 547 PHE 0.011 0.001 PHE C 688 TYR 0.019 0.001 TYR B1046 ARG 0.011 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 2.215 Fit side-chains REVERT: A 898 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7872 (pp30) REVERT: A 1084 SER cc_start: 0.8728 (m) cc_final: 0.8478 (t) REVERT: A 1088 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 1008 LEU cc_start: 0.8701 (tp) cc_final: 0.8495 (tp) REVERT: B 1016 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6806 (ttp-170) REVERT: B 1020 ASP cc_start: 0.8384 (t0) cc_final: 0.8016 (m-30) REVERT: C 250 ASP cc_start: 0.7282 (t0) cc_final: 0.7035 (t0) outliers start: 50 outliers final: 33 residues processed: 158 average time/residue: 0.2945 time to fit residues: 72.5266 Evaluate side-chains 152 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1016 ARG Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 195 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 849 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17100 Z= 0.196 Angle : 0.546 15.615 23223 Z= 0.279 Chirality : 0.043 0.188 2468 Planarity : 0.004 0.056 3007 Dihedral : 4.757 30.890 2236 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 2.69 % Allowed : 15.53 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2037 helix: 0.04 (0.29), residues: 325 sheet: -0.84 (0.20), residues: 643 loop : -1.27 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 257 HIS 0.005 0.001 HIS A 899 PHE 0.012 0.001 PHE C 688 TYR 0.021 0.001 TYR B1046 ARG 0.011 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 122 time to evaluate : 1.966 Fit side-chains REVERT: A 898 GLN cc_start: 0.8480 (pp30) cc_final: 0.7708 (pp30) REVERT: A 1084 SER cc_start: 0.8727 (m) cc_final: 0.8485 (t) REVERT: A 1088 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 1016 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6912 (ttp-170) REVERT: B 1020 ASP cc_start: 0.8352 (t0) cc_final: 0.8013 (m-30) REVERT: C 250 ASP cc_start: 0.7254 (t0) cc_final: 0.7009 (t0) outliers start: 49 outliers final: 37 residues processed: 154 average time/residue: 0.2877 time to fit residues: 68.4656 Evaluate side-chains 157 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1016 ARG Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17100 Z= 0.150 Angle : 0.536 15.163 23223 Z= 0.274 Chirality : 0.043 0.189 2468 Planarity : 0.004 0.060 3007 Dihedral : 4.620 31.089 2236 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.25 % Allowed : 16.08 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2037 helix: 0.25 (0.30), residues: 324 sheet: -0.69 (0.21), residues: 643 loop : -1.21 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 758 HIS 0.008 0.001 HIS C 225 PHE 0.010 0.001 PHE C 688 TYR 0.016 0.001 TYR B1046 ARG 0.012 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8535 (pp30) cc_final: 0.7878 (pp30) REVERT: A 1084 SER cc_start: 0.8702 (m) cc_final: 0.8439 (t) REVERT: A 1089 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: B 1016 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7004 (ttp-170) REVERT: B 1020 ASP cc_start: 0.8319 (t0) cc_final: 0.8010 (m-30) REVERT: C 250 ASP cc_start: 0.7168 (t0) cc_final: 0.6908 (t0) outliers start: 41 outliers final: 33 residues processed: 156 average time/residue: 0.2891 time to fit residues: 69.9322 Evaluate side-chains 158 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1016 ARG Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 0.0770 chunk 172 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN C 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17100 Z= 0.207 Angle : 0.551 14.982 23223 Z= 0.280 Chirality : 0.043 0.188 2468 Planarity : 0.004 0.058 3007 Dihedral : 4.643 30.689 2236 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 2.20 % Allowed : 16.25 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2037 helix: 0.29 (0.30), residues: 324 sheet: -0.62 (0.21), residues: 649 loop : -1.18 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 888 HIS 0.004 0.001 HIS D 561 PHE 0.012 0.001 PHE C 688 TYR 0.021 0.001 TYR B1046 ARG 0.012 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: D 53 HIS cc_start: 0.7888 (m-70) cc_final: 0.7326 (m170) REVERT: A 898 GLN cc_start: 0.8530 (pp30) cc_final: 0.7928 (pp30) REVERT: A 1000 GLU cc_start: 0.7429 (tp30) cc_final: 0.7166 (tp30) REVERT: A 1084 SER cc_start: 0.8683 (m) cc_final: 0.8450 (t) REVERT: A 1089 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 1016 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7012 (ttp-170) REVERT: B 1020 ASP cc_start: 0.8318 (t0) cc_final: 0.8009 (m-30) REVERT: C 250 ASP cc_start: 0.7229 (t0) cc_final: 0.6958 (t0) outliers start: 40 outliers final: 37 residues processed: 150 average time/residue: 0.3049 time to fit residues: 70.1286 Evaluate side-chains 158 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1016 ARG Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN C 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17100 Z= 0.217 Angle : 0.558 16.059 23223 Z= 0.283 Chirality : 0.044 0.189 2468 Planarity : 0.004 0.060 3007 Dihedral : 4.667 30.608 2236 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 2.09 % Allowed : 16.47 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 2037 helix: 0.35 (0.30), residues: 324 sheet: -0.55 (0.21), residues: 651 loop : -1.19 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 888 HIS 0.005 0.001 HIS C 741 PHE 0.012 0.001 PHE C 688 TYR 0.020 0.001 TYR B1046 ARG 0.015 0.000 ARG C 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8000 (pp30) REVERT: A 997 LEU cc_start: 0.6738 (pt) cc_final: 0.6402 (tp) REVERT: A 1084 SER cc_start: 0.8695 (m) cc_final: 0.8475 (t) REVERT: A 1105 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7515 (mmtm) REVERT: B 1016 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7000 (ttp-170) REVERT: B 1020 ASP cc_start: 0.8307 (t0) cc_final: 0.7983 (m-30) REVERT: C 250 ASP cc_start: 0.7273 (t0) cc_final: 0.7003 (t0) REVERT: C 557 MET cc_start: 0.7968 (ptp) cc_final: 0.7662 (mtm) outliers start: 38 outliers final: 35 residues processed: 145 average time/residue: 0.3003 time to fit residues: 66.7404 Evaluate side-chains 155 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1016 ARG Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 0.0170 chunk 161 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066160 restraints weight = 42682.670| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.10 r_work: 0.3003 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17100 Z= 0.212 Angle : 0.774 59.176 23223 Z= 0.433 Chirality : 0.048 1.022 2468 Planarity : 0.004 0.059 3007 Dihedral : 4.661 30.629 2236 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 2.20 % Allowed : 16.41 % Favored : 81.39 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 2037 helix: 0.36 (0.30), residues: 324 sheet: -0.55 (0.21), residues: 651 loop : -1.19 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 888 HIS 0.005 0.001 HIS C 741 PHE 0.012 0.001 PHE C 688 TYR 0.018 0.001 TYR B1046 ARG 0.013 0.000 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.51 seconds wall clock time: 59 minutes 47.37 seconds (3587.37 seconds total)