Starting phenix.real_space_refine on Mon Mar 18 21:32:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7b_24882/03_2024/7s7b_24882.pdb" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 sd= 1.240 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 Zn 2 6.06 5 P 22 5.49 5 S 134 5.16 5 C 14071 2.51 5 N 3795 2.21 5 O 4193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22217 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "B" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2847 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'TRANS': 328} Chain breaks: 4 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "D" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 4} Chain breaks: 1 Chain: "E" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "F" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2856 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain breaks: 4 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "H" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 6, 'rna3p': 4} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8786 SG CYS B 229 69.092 81.069 150.591 1.00230.03 S ATOM 8811 SG CYS B 232 68.012 81.919 147.188 1.00229.84 S ATOM 8889 SG CYS B 242 70.870 83.686 148.641 1.00233.19 S ATOM 19898 SG CYS F 229 30.303 83.287 78.681 1.00219.13 S ATOM 19923 SG CYS F 232 32.475 84.891 81.330 1.00222.29 S ATOM 20001 SG CYS F 242 29.074 86.148 80.707 1.00223.04 S Time building chain proxies: 11.05, per 1000 atoms: 0.50 Number of scatterers: 22217 At special positions: 0 Unit cell: (104.448, 154.496, 228.48, 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) Zn 2 29.99 S 134 16.00 P 22 15.00 O 4193 8.00 N 3795 7.00 C 14071 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: 9.02 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 900 " pdb="ZN ZN B 900 " - pdb=" NE2 HIS B 237 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 229 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 232 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 242 " pdb=" ZN F 900 " pdb="ZN ZN F 900 " - pdb=" NE2 HIS F 237 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 229 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 242 " pdb="ZN ZN F 900 " - pdb=" SG CYS F 232 " Number of angles added : 6 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 15 sheets defined 49.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.586A pdb=" N ASN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.831A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.531A pdb=" N ARG A 258 " --> pdb=" O HIS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.668A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.663A pdb=" N PHE A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 372 through 384 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.598A pdb=" N VAL A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Proline residue: A 446 - end of helix Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 580 through 588 removed outlier: 3.971A pdb=" N MET A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 615 removed outlier: 3.765A pdb=" N HIS A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Proline residue: A 599 - end of helix Processing helix chain 'A' and resid 619 through 645 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.589A pdb=" N LEU A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.993A pdb=" N LEU A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.873A pdb=" N LYS A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 843 removed outlier: 3.910A pdb=" N VAL A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 861 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.967A pdb=" N GLU A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 894 Processing helix chain 'A' and resid 901 through 913 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 954 through 962 removed outlier: 4.319A pdb=" N PHE A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 978 through 984 Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1016 through 1030 Processing helix chain 'B' and resid 47 through 74 Processing helix chain 'B' and resid 102 through 130 removed outlier: 5.882A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.106A pdb=" N GLU B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.120A pdb=" N TYR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.607A pdb=" N LEU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 326 " --> pdb=" O TRP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.686A pdb=" N PHE B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.872A pdb=" N GLN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.621A pdb=" N ASN E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 181 removed outlier: 3.963A pdb=" N ALA E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 207 Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 241 through 245 removed outlier: 4.345A pdb=" N GLU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 245' Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.654A pdb=" N ARG E 258 " --> pdb=" O HIS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 273 removed outlier: 3.765A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.765A pdb=" N PHE E 292 " --> pdb=" O ASN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 372 through 384 Processing helix chain 'E' and resid 395 through 406 Processing helix chain 'E' and resid 413 through 429 Processing helix chain 'E' and resid 432 through 437 Processing helix chain 'E' and resid 438 through 451 removed outlier: 3.816A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Proline residue: E 446 - end of helix Processing helix chain 'E' and resid 460 through 473 Processing helix chain 'E' and resid 483 through 488 Processing helix chain 'E' and resid 513 through 522 Processing helix chain 'E' and resid 544 through 554 Processing helix chain 'E' and resid 566 through 576 Processing helix chain 'E' and resid 580 through 588 removed outlier: 4.044A pdb=" N MET E 584 " --> pdb=" O ASN E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 615 Proline residue: E 599 - end of helix Processing helix chain 'E' and resid 619 through 645 removed outlier: 3.584A pdb=" N VAL E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 652 through 654 No H-bonds generated for 'chain 'E' and resid 652 through 654' Processing helix chain 'E' and resid 752 through 770 removed outlier: 3.973A pdb=" N ARG E 756 " --> pdb=" O PRO E 752 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 757 " --> pdb=" O VAL E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 807 removed outlier: 3.894A pdb=" N LYS E 791 " --> pdb=" O ASP E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 812 removed outlier: 4.468A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 812 " --> pdb=" O PRO E 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 807 through 812' Processing helix chain 'E' and resid 814 through 843 removed outlier: 3.927A pdb=" N VAL E 818 " --> pdb=" O ASN E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 861 Processing helix chain 'E' and resid 871 through 880 removed outlier: 4.123A pdb=" N GLU E 879 " --> pdb=" O ARG E 875 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE E 880 " --> pdb=" O VAL E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 885 through 894 Processing helix chain 'E' and resid 895 through 899 removed outlier: 3.951A pdb=" N ASP E 899 " --> pdb=" O LEU E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 913 Processing helix chain 'E' and resid 929 through 949 Processing helix chain 'E' and resid 954 through 962 removed outlier: 4.332A pdb=" N PHE E 962 " --> pdb=" O TYR E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 976 Processing helix chain 'E' and resid 978 through 984 Processing helix chain 'E' and resid 989 through 1015 Processing helix chain 'E' and resid 1016 through 1030 Processing helix chain 'F' and resid 47 through 75 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 108 through 130 Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.845A pdb=" N ARG F 282 " --> pdb=" O VAL F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 300 Processing helix chain 'F' and resid 307 through 317 removed outlier: 4.061A pdb=" N TYR F 311 " --> pdb=" O PRO F 307 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 312 " --> pdb=" O PRO F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 326 removed outlier: 4.078A pdb=" N GLU F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 364 removed outlier: 3.733A pdb=" N LEU F 364 " --> pdb=" O LEU F 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 364' Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.118A pdb=" N LEU F 403 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 667 removed outlier: 3.661A pdb=" N PHE F 666 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 667 " --> pdb=" O MET F 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 662 through 667' Processing helix chain 'F' and resid 683 through 692 removed outlier: 3.596A pdb=" N LEU F 692 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 700 Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.911A pdb=" N GLN G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY G 34 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 70 removed outlier: 4.278A pdb=" N TYR G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.633A pdb=" N TYR A 308 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 157 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG A 184 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 249 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 186 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE A 251 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 188 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 189 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.683A pdb=" N GLY A 453 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 390 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 496 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N MET A 538 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 498 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN A 317 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 537 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 319 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 539 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 321 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 320 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU A 330 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 328 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 328 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 504 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 732 removed outlier: 5.821A pdb=" N LEU A 699 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 674 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 668 " --> pdb=" O ASN A 664 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN A 664 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 670 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 662 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 663 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 736 " --> pdb=" O LYS A 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 182 removed outlier: 4.762A pdb=" N PHE F 99 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER B 171 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE F 97 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 173 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 95 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 97 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER F 171 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.644A pdb=" N ASN C 56 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 39 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE C 54 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 99 through 102 removed outlier: 3.533A pdb=" N TYR E 308 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL E 157 " --> pdb=" O PHE E 281 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER E 283 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 159 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA E 247 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 280 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL E 249 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 282 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE E 251 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG E 184 " --> pdb=" O TRP E 248 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE E 250 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE E 186 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP E 252 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR E 188 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 211 through 212 Processing sheet with id=AB2, first strand: chain 'E' and resid 453 through 455 removed outlier: 6.707A pdb=" N GLY E 453 " --> pdb=" O PHE E 480 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 496 " --> pdb=" O ILE E 536 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N MET E 538 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE E 498 " --> pdb=" O MET E 538 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN E 317 " --> pdb=" O VAL E 535 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 537 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR E 319 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL E 539 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE E 321 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 320 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 330 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU E 328 " --> pdb=" O PRO E 322 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 328 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 502 through 504 Processing sheet with id=AB4, first strand: chain 'E' and resid 727 through 732 removed outlier: 3.539A pdb=" N ASN E 676 " --> pdb=" O GLU E 697 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 699 " --> pdb=" O VAL E 674 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 674 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN E 664 " --> pdb=" O ASP E 668 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY E 670 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 662 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS E 663 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU E 736 " --> pdb=" O LYS E 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 327 through 328 Processing sheet with id=AB6, first strand: chain 'G' and resid 36 through 40 removed outlier: 3.569A pdb=" N ILE G 80 " --> pdb=" O ILE G 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE G 73 " --> pdb=" O ILE G 80 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2832 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: 7.68 Time building geometry restraints manager: 9.70 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: 7206 1.34 - 1.45: 2775 1.45 - 1.57: 12462 1.57 - 1.69: 40 1.69 - 1.81: 218 Bond restraints: 22701 Sorted by residual: bond pdb=" C MET A 543 " pdb=" N SER A 544 " ideal model delta sigma weight residual 1.340 1.276 0.065 5.87e-02 2.90e+02 1.22e+00 bond pdb=" CB TRP A 266 " pdb=" CG TRP A 266 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.77e-01 bond pdb=" CG GLN A 655 " pdb=" CD GLN A 655 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.43e-01 bond pdb=" CB ARG E 743 " pdb=" CG ARG E 743 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.32e-01 bond pdb=" CG GLN E 655 " pdb=" CD GLN E 655 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 6.89e-01 ... (remaining 22696 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 842 106.51 - 113.39: 12353 113.39 - 120.27: 8408 120.27 - 127.15: 8823 127.15 - 134.03: 290 Bond angle restraints: 30716 Sorted by residual: angle pdb=" N ASP A1033 " pdb=" CA ASP A1033 " pdb=" C ASP A1033 " ideal model delta sigma weight residual 111.37 115.19 -3.82 1.64e+00 3.72e-01 5.42e+00 angle pdb=" N ILE B 94 " pdb=" CA ILE B 94 " pdb=" C ILE B 94 " ideal model delta sigma weight residual 109.34 104.73 4.61 2.08e+00 2.31e-01 4.91e+00 angle pdb=" N GLN F 107 " pdb=" CA GLN F 107 " pdb=" C GLN F 107 " ideal model delta sigma weight residual 111.36 113.77 -2.41 1.09e+00 8.42e-01 4.88e+00 angle pdb=" N ASP E1033 " pdb=" CA ASP E1033 " pdb=" C ASP E1033 " ideal model delta sigma weight residual 111.02 113.31 -2.29 1.22e+00 6.72e-01 3.53e+00 angle pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" C TYR A 590 " ideal model delta sigma weight residual 113.18 110.80 2.38 1.33e+00 5.65e-01 3.20e+00 ... (remaining 30711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 13363 20.79 - 41.59: 473 41.59 - 62.38: 73 62.38 - 83.17: 9 83.17 - 103.96: 2 Dihedral angle restraints: 13920 sinusoidal: 6003 harmonic: 7917 Sorted by residual: dihedral pdb=" CA ARG A1032 " pdb=" C ARG A1032 " pdb=" N ASP A1033 " pdb=" CA ASP A1033 " ideal model delta harmonic sigma weight residual 180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ARG E1032 " pdb=" C ARG E1032 " pdb=" N ASP E1033 " pdb=" CA ASP E1033 " ideal model delta harmonic sigma weight residual 180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP E1033 " pdb=" C ASP E1033 " pdb=" N ILE E1034 " pdb=" CA ILE E1034 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 13917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2149 0.028 - 0.057: 846 0.057 - 0.085: 211 0.085 - 0.114: 159 0.114 - 0.142: 50 Chirality restraints: 3415 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA GLN A 387 " pdb=" N GLN A 387 " pdb=" C GLN A 387 " pdb=" CB GLN A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 660 " pdb=" N ILE B 660 " pdb=" C ILE B 660 " pdb=" CB ILE B 660 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 3412 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 387 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO E 388 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 388 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 388 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 311 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C TYR F 311 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR F 311 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG F 312 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 200 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 201 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " -0.021 5.00e-02 4.00e+02 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 262 2.55 - 3.14: 19687 3.14 - 3.73: 33684 3.73 - 4.31: 46329 4.31 - 4.90: 78312 Nonbonded interactions: 178274 Sorted by model distance: nonbonded pdb=" OG1 THR A 228 " pdb=" OP1 A D 46 " model vdw 1.963 2.440 nonbonded pdb=" OE2 GLU E 267 " pdb=" OG SER E 561 " model vdw 1.976 2.440 nonbonded pdb=" O THR E 972 " pdb=" OG1 THR E 975 " model vdw 2.022 2.440 nonbonded pdb=" O THR A 972 " pdb=" OG1 THR A 975 " model vdw 2.067 2.440 nonbonded pdb=" N GLU E 230 " pdb=" OE1 GLU E 230 " model vdw 2.098 2.520 ... (remaining 178269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 46 through 216 or resid 228 through 701 or resid 900)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.520 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 61.590 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 0.065 22701 Z= 0.239 Angle : 0.463 5.359 30716 Z= 0.243 Chirality : 0.039 0.142 3415 Planarity : 0.003 0.045 3898 Dihedral : 10.889 103.962 8778 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.54 % Allowed : 5.81 % Favored : 92.65 % 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: 0.42 (0.17), residues: 2673 helix: 1.80 (0.15), residues: 1211 sheet: -0.78 (0.36), residues: 242 loop : -1.09 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 295 HIS 0.003 0.001 HIS F 109 PHE 0.011 0.001 PHE E 770 TYR 0.012 0.001 TYR E 612 ARG 0.002 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 445 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8696 (mmt) cc_final: 0.8246 (mmp) REVERT: A 387 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: A 529 MET cc_start: 0.8243 (ptp) cc_final: 0.7935 (ptp) REVERT: A 643 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7147 (t80) REVERT: A 837 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8258 (tmm-80) REVERT: A 891 MET cc_start: 0.8946 (mtm) cc_final: 0.8673 (mtm) REVERT: B 57 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 124 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 163 LYS cc_start: 0.8383 (mttt) cc_final: 0.8171 (tttp) REVERT: B 303 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8506 (p0) REVERT: B 382 TRP cc_start: 0.9339 (p-90) cc_final: 0.9020 (p90) REVERT: C 30 PHE cc_start: 0.9189 (m-10) cc_final: 0.8944 (m-10) REVERT: C 57 PHE cc_start: 0.7806 (m-80) cc_final: 0.7493 (m-10) REVERT: C 59 HIS cc_start: 0.8630 (m-70) cc_final: 0.8252 (m-70) REVERT: C 74 LYS cc_start: 0.8673 (tppp) cc_final: 0.8359 (mmmm) REVERT: E 172 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8639 (mt-10) REVERT: E 240 SER cc_start: 0.8953 (t) cc_final: 0.8464 (t) REVERT: E 387 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: E 393 SER cc_start: 0.8896 (t) cc_final: 0.8693 (p) REVERT: E 395 SER cc_start: 0.8842 (t) cc_final: 0.8323 (p) REVERT: E 398 ASP cc_start: 0.8797 (m-30) cc_final: 0.8127 (m-30) REVERT: E 408 LYS cc_start: 0.9062 (ptmm) cc_final: 0.8439 (ptmm) REVERT: E 473 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 500 ASN cc_start: 0.8445 (t0) cc_final: 0.8146 (t0) REVERT: E 529 MET cc_start: 0.8215 (ptp) cc_final: 0.7982 (ptm) REVERT: E 537 LEU cc_start: 0.9602 (tp) cc_final: 0.9390 (tt) REVERT: E 542 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8673 (mtmm) REVERT: E 620 GLU cc_start: 0.7522 (pt0) cc_final: 0.7059 (mp0) REVERT: E 713 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8426 (tp30) REVERT: E 725 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7359 (tm-30) REVERT: E 754 ASP cc_start: 0.8457 (t0) cc_final: 0.8153 (t0) REVERT: E 772 ASP cc_start: 0.7931 (p0) cc_final: 0.7289 (p0) REVERT: E 778 ASP cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) REVERT: E 878 CYS cc_start: 0.8567 (m) cc_final: 0.8137 (m) REVERT: E 890 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 1001 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 1002 GLU cc_start: 0.8896 (pt0) cc_final: 0.8566 (pt0) REVERT: F 55 GLN cc_start: 0.7721 (tp40) cc_final: 0.7272 (pp30) REVERT: F 161 ASN cc_start: 0.7844 (m-40) cc_final: 0.7577 (m-40) REVERT: F 163 LYS cc_start: 0.8171 (mttt) cc_final: 0.7958 (pttp) REVERT: F 185 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: F 274 TYR cc_start: 0.8672 (p90) cc_final: 0.8458 (p90) REVERT: F 390 MET cc_start: 0.2414 (ttp) cc_final: 0.2021 (ttt) REVERT: F 677 ASN cc_start: 0.9095 (m-40) cc_final: 0.8866 (m110) REVERT: G 11 THR cc_start: 0.5864 (p) cc_final: 0.5650 (p) REVERT: G 31 HIS cc_start: 0.8600 (t70) cc_final: 0.8211 (p90) REVERT: G 52 PHE cc_start: 0.3927 (OUTLIER) cc_final: 0.3658 (p90) outliers start: 37 outliers final: 14 residues processed: 475 average time/residue: 0.3735 time to fit residues: 265.3676 Evaluate side-chains 344 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 324 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 3.9990 chunk 204 optimal weight: 0.0170 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 426 ASN E 519 GLN E 795 GLN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 915 GLN F 102 ASN F 126 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 HIS F 238 GLN F 271 GLN F 330 ASN F 698 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22701 Z= 0.208 Angle : 0.600 11.707 30716 Z= 0.302 Chirality : 0.043 0.188 3415 Planarity : 0.004 0.103 3898 Dihedral : 7.800 100.723 3189 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % 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 (0.17), residues: 2673 helix: 1.81 (0.15), residues: 1240 sheet: -0.19 (0.38), residues: 222 loop : -0.97 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 266 HIS 0.010 0.001 HIS E 807 PHE 0.017 0.001 PHE C 52 TYR 0.021 0.001 TYR E 402 ARG 0.007 0.000 ARG E 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 MET cc_start: 0.9065 (mtm) cc_final: 0.8762 (mtm) REVERT: A 935 MET cc_start: 0.8579 (tmm) cc_final: 0.8170 (tmm) REVERT: B 57 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7412 (mm-30) REVERT: B 163 LYS cc_start: 0.8401 (mttt) cc_final: 0.8152 (tttp) REVERT: B 313 MET cc_start: 0.8516 (ptt) cc_final: 0.8124 (ppp) REVERT: B 382 TRP cc_start: 0.9330 (p-90) cc_final: 0.8985 (p90) REVERT: B 663 MET cc_start: 0.8274 (ttm) cc_final: 0.7997 (ttt) REVERT: C 30 PHE cc_start: 0.9224 (m-10) cc_final: 0.8945 (m-10) REVERT: C 57 PHE cc_start: 0.7813 (m-80) cc_final: 0.7608 (m-10) REVERT: E 172 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8526 (mt-10) REVERT: E 240 SER cc_start: 0.8563 (t) cc_final: 0.7766 (t) REVERT: E 406 MET cc_start: 0.9109 (mmp) cc_final: 0.8774 (mmp) REVERT: E 491 MET cc_start: 0.8457 (mtt) cc_final: 0.8236 (mtt) REVERT: E 500 ASN cc_start: 0.8481 (t0) cc_final: 0.8192 (t0) REVERT: E 542 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8632 (mtmm) REVERT: E 620 GLU cc_start: 0.7495 (pt0) cc_final: 0.7098 (mp0) REVERT: E 665 GLU cc_start: 0.7877 (pp20) cc_final: 0.7616 (pp20) REVERT: E 680 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7160 (tptp) REVERT: E 713 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8410 (tp30) REVERT: E 725 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7626 (tp30) REVERT: E 754 ASP cc_start: 0.8261 (t0) cc_final: 0.7896 (t0) REVERT: E 772 ASP cc_start: 0.7839 (p0) cc_final: 0.7175 (p0) REVERT: E 778 ASP cc_start: 0.8879 (t0) cc_final: 0.8650 (t0) REVERT: E 878 CYS cc_start: 0.8511 (m) cc_final: 0.8205 (m) REVERT: E 890 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8561 (mm-30) REVERT: E 987 ASP cc_start: 0.8867 (p0) cc_final: 0.8650 (p0) REVERT: E 1001 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 1002 GLU cc_start: 0.8783 (pt0) cc_final: 0.8494 (pt0) REVERT: E 1031 LYS cc_start: 0.8937 (tptm) cc_final: 0.8593 (tptm) REVERT: E 1036 PHE cc_start: 0.9019 (m-80) cc_final: 0.8779 (m-80) REVERT: F 57 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8140 (pt0) REVERT: F 161 ASN cc_start: 0.7775 (m-40) cc_final: 0.7488 (m-40) REVERT: G 31 HIS cc_start: 0.8455 (t70) cc_final: 0.8113 (p-80) REVERT: G 75 LEU cc_start: 0.8431 (mp) cc_final: 0.8229 (mp) REVERT: G 78 ARG cc_start: 0.8035 (ttt180) cc_final: 0.6866 (mmm160) outliers start: 2 outliers final: 1 residues processed: 409 average time/residue: 0.3376 time to fit residues: 213.7308 Evaluate side-chains 316 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 204 optimal weight: 0.0770 chunk 166 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 245 optimal weight: 0.5980 chunk 265 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 197 optimal weight: 0.0870 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 126 GLN F 228 HIS F 330 ASN G 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22701 Z= 0.182 Angle : 0.550 11.654 30716 Z= 0.278 Chirality : 0.042 0.182 3415 Planarity : 0.004 0.050 3898 Dihedral : 7.726 106.066 3189 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.12 % Allowed : 2.86 % Favored : 97.01 % 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: 0.61 (0.17), residues: 2673 helix: 1.80 (0.15), residues: 1239 sheet: -0.29 (0.37), residues: 232 loop : -0.97 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.006 0.001 HIS G 59 PHE 0.027 0.001 PHE C 52 TYR 0.024 0.001 TYR G 65 ARG 0.008 0.000 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 MET cc_start: 0.8839 (ttm) cc_final: 0.8637 (ttm) REVERT: A 891 MET cc_start: 0.8991 (mtm) cc_final: 0.8691 (mtm) REVERT: A 935 MET cc_start: 0.8608 (tmm) cc_final: 0.8153 (tmm) REVERT: B 49 LEU cc_start: 0.7616 (mt) cc_final: 0.7386 (mt) REVERT: B 57 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 163 LYS cc_start: 0.8385 (mttt) cc_final: 0.8146 (tttp) REVERT: B 283 PHE cc_start: 0.7040 (p90) cc_final: 0.6810 (p90) REVERT: B 313 MET cc_start: 0.8576 (ptt) cc_final: 0.8145 (ppp) REVERT: B 382 TRP cc_start: 0.9326 (p-90) cc_final: 0.8956 (p90) REVERT: B 663 MET cc_start: 0.8281 (ttm) cc_final: 0.8009 (ttt) REVERT: C 57 PHE cc_start: 0.7825 (m-80) cc_final: 0.7619 (m-10) REVERT: E 172 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8539 (mt-10) REVERT: E 233 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7253 (ttt-90) REVERT: E 240 SER cc_start: 0.8481 (t) cc_final: 0.8091 (t) REVERT: E 395 SER cc_start: 0.8425 (t) cc_final: 0.8178 (t) REVERT: E 398 ASP cc_start: 0.8650 (m-30) cc_final: 0.8318 (m-30) REVERT: E 406 MET cc_start: 0.9301 (mmp) cc_final: 0.8865 (mmp) REVERT: E 408 LYS cc_start: 0.9251 (ptmt) cc_final: 0.8985 (ptmm) REVERT: E 491 MET cc_start: 0.8482 (mtt) cc_final: 0.8214 (mtt) REVERT: E 497 LEU cc_start: 0.9556 (tp) cc_final: 0.9314 (tt) REVERT: E 500 ASN cc_start: 0.8485 (t0) cc_final: 0.8195 (t0) REVERT: E 542 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8549 (mtmm) REVERT: E 620 GLU cc_start: 0.7524 (pt0) cc_final: 0.7152 (mp0) REVERT: E 680 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7158 (tptp) REVERT: E 713 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8380 (tp30) REVERT: E 725 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7589 (tp30) REVERT: E 754 ASP cc_start: 0.8248 (t0) cc_final: 0.8022 (t0) REVERT: E 765 GLU cc_start: 0.8055 (tp30) cc_final: 0.7743 (tp30) REVERT: E 772 ASP cc_start: 0.7774 (p0) cc_final: 0.7052 (p0) REVERT: E 778 ASP cc_start: 0.8884 (t0) cc_final: 0.8646 (t0) REVERT: E 878 CYS cc_start: 0.8424 (m) cc_final: 0.8047 (m) REVERT: E 890 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8632 (mm-30) REVERT: E 1001 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8083 (tm-30) REVERT: E 1002 GLU cc_start: 0.8782 (pt0) cc_final: 0.8532 (pt0) REVERT: E 1007 MET cc_start: 0.9167 (mmm) cc_final: 0.8759 (mmm) REVERT: F 55 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7132 (pp30) REVERT: F 57 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8087 (pt0) REVERT: F 66 GLU cc_start: 0.6902 (mp0) cc_final: 0.6626 (mp0) REVERT: F 161 ASN cc_start: 0.7773 (m-40) cc_final: 0.7512 (m-40) REVERT: F 163 LYS cc_start: 0.8321 (tttm) cc_final: 0.7398 (pttp) REVERT: F 239 MET cc_start: 0.7034 (mmm) cc_final: 0.6511 (mmm) REVERT: F 274 TYR cc_start: 0.9067 (p90) cc_final: 0.8863 (p90) REVERT: G 31 HIS cc_start: 0.8434 (t70) cc_final: 0.8119 (p-80) outliers start: 3 outliers final: 0 residues processed: 393 average time/residue: 0.3387 time to fit residues: 208.0750 Evaluate side-chains 311 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 572 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 231 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 126 GLN G 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 22701 Z= 0.486 Angle : 0.669 11.107 30716 Z= 0.341 Chirality : 0.046 0.206 3415 Planarity : 0.005 0.055 3898 Dihedral : 7.980 106.761 3189 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2673 helix: 1.51 (0.15), residues: 1247 sheet: -0.31 (0.37), residues: 232 loop : -1.14 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 266 HIS 0.007 0.001 HIS E 594 PHE 0.020 0.002 PHE G 52 TYR 0.023 0.002 TYR G 65 ARG 0.005 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 MET cc_start: 0.9081 (mtm) cc_final: 0.8781 (mtm) REVERT: A 935 MET cc_start: 0.8564 (tmm) cc_final: 0.8099 (tmm) REVERT: B 49 LEU cc_start: 0.7571 (mt) cc_final: 0.7344 (mt) REVERT: B 57 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 163 LYS cc_start: 0.8444 (mttt) cc_final: 0.8168 (tttp) REVERT: B 283 PHE cc_start: 0.6895 (p90) cc_final: 0.6643 (p90) REVERT: B 313 MET cc_start: 0.8558 (ptt) cc_final: 0.8226 (ppp) REVERT: B 382 TRP cc_start: 0.9381 (p-90) cc_final: 0.9006 (p90) REVERT: B 399 PHE cc_start: 0.8572 (t80) cc_final: 0.8327 (t80) REVERT: C 59 HIS cc_start: 0.8621 (m-70) cc_final: 0.8145 (m-70) REVERT: E 172 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8601 (mt-10) REVERT: E 197 GLN cc_start: 0.8841 (mt0) cc_final: 0.8608 (mt0) REVERT: E 228 THR cc_start: 0.9246 (p) cc_final: 0.8927 (p) REVERT: E 236 LEU cc_start: 0.9097 (mm) cc_final: 0.8892 (mm) REVERT: E 240 SER cc_start: 0.8479 (t) cc_final: 0.7819 (t) REVERT: E 252 ASP cc_start: 0.8888 (t0) cc_final: 0.8680 (t0) REVERT: E 398 ASP cc_start: 0.8681 (m-30) cc_final: 0.8408 (m-30) REVERT: E 402 TYR cc_start: 0.9009 (m-80) cc_final: 0.8776 (m-80) REVERT: E 406 MET cc_start: 0.9239 (mmp) cc_final: 0.8670 (mmp) REVERT: E 408 LYS cc_start: 0.9302 (ptmt) cc_final: 0.9027 (ptmm) REVERT: E 438 LEU cc_start: 0.9247 (mt) cc_final: 0.9023 (mm) REVERT: E 500 ASN cc_start: 0.8716 (t0) cc_final: 0.8425 (t0) REVERT: E 542 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8635 (mtmm) REVERT: E 550 GLN cc_start: 0.8727 (mt0) cc_final: 0.8430 (mt0) REVERT: E 584 MET cc_start: 0.8859 (tpp) cc_final: 0.8513 (tpp) REVERT: E 620 GLU cc_start: 0.7554 (pt0) cc_final: 0.7188 (mp0) REVERT: E 680 LYS cc_start: 0.7827 (tmtt) cc_final: 0.7339 (tptp) REVERT: E 713 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8461 (tp30) REVERT: E 765 GLU cc_start: 0.8121 (tp30) cc_final: 0.7790 (tp30) REVERT: E 772 ASP cc_start: 0.7934 (p0) cc_final: 0.7287 (p0) REVERT: E 778 ASP cc_start: 0.8950 (t0) cc_final: 0.8711 (t0) REVERT: E 878 CYS cc_start: 0.8537 (m) cc_final: 0.8138 (m) REVERT: E 890 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8743 (mm-30) REVERT: E 999 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7592 (tpp80) REVERT: E 1001 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 1007 MET cc_start: 0.9194 (mmm) cc_final: 0.8792 (mmm) REVERT: F 55 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7200 (pp30) REVERT: F 57 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8061 (pt0) REVERT: F 66 GLU cc_start: 0.6870 (mp0) cc_final: 0.6213 (mp0) REVERT: F 161 ASN cc_start: 0.7762 (m-40) cc_final: 0.7466 (m-40) REVERT: F 239 MET cc_start: 0.7302 (mmm) cc_final: 0.6758 (mmm) REVERT: F 299 LEU cc_start: 0.8946 (tp) cc_final: 0.8724 (pp) REVERT: F 399 PHE cc_start: 0.7824 (t80) cc_final: 0.7484 (t80) REVERT: F 677 ASN cc_start: 0.9204 (m110) cc_final: 0.8985 (m110) REVERT: G 31 HIS cc_start: 0.8459 (t70) cc_final: 0.8147 (p-80) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.3280 time to fit residues: 185.0455 Evaluate side-chains 303 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS B 231 ASN C 56 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 126 GLN G 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22701 Z= 0.206 Angle : 0.551 11.868 30716 Z= 0.279 Chirality : 0.042 0.198 3415 Planarity : 0.004 0.051 3898 Dihedral : 7.802 105.068 3189 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.01 % 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: 0.49 (0.17), residues: 2673 helix: 1.70 (0.15), residues: 1237 sheet: -0.14 (0.37), residues: 228 loop : -1.06 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 322 HIS 0.011 0.001 HIS E 807 PHE 0.018 0.001 PHE G 52 TYR 0.019 0.001 TYR G 65 ARG 0.004 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 MET cc_start: 0.8998 (mtm) cc_final: 0.8740 (mtm) REVERT: A 935 MET cc_start: 0.8566 (tmm) cc_final: 0.8148 (tmm) REVERT: B 49 LEU cc_start: 0.7523 (mt) cc_final: 0.7313 (mt) REVERT: B 57 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7597 (mm-30) REVERT: B 163 LYS cc_start: 0.8386 (mttt) cc_final: 0.8122 (tttt) REVERT: B 239 MET cc_start: 0.3860 (tpp) cc_final: 0.1445 (tmm) REVERT: B 283 PHE cc_start: 0.7201 (p90) cc_final: 0.6981 (p90) REVERT: B 286 PHE cc_start: 0.7503 (m-80) cc_final: 0.7026 (m-80) REVERT: B 313 MET cc_start: 0.8472 (ptt) cc_final: 0.8090 (ppp) REVERT: B 382 TRP cc_start: 0.9352 (p-90) cc_final: 0.8963 (p90) REVERT: B 678 MET cc_start: 0.8670 (tpt) cc_final: 0.8437 (tpt) REVERT: C 59 HIS cc_start: 0.8644 (m-70) cc_final: 0.8252 (m-70) REVERT: E 172 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8573 (mt-10) REVERT: E 197 GLN cc_start: 0.8793 (mt0) cc_final: 0.8541 (mt0) REVERT: E 240 SER cc_start: 0.8558 (t) cc_final: 0.7656 (t) REVERT: E 398 ASP cc_start: 0.8617 (m-30) cc_final: 0.8352 (m-30) REVERT: E 406 MET cc_start: 0.9261 (mmp) cc_final: 0.8651 (mmp) REVERT: E 408 LYS cc_start: 0.9233 (ptmt) cc_final: 0.9000 (ptmm) REVERT: E 500 ASN cc_start: 0.8493 (t0) cc_final: 0.8225 (t0) REVERT: E 542 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8616 (mtmm) REVERT: E 550 GLN cc_start: 0.8686 (mt0) cc_final: 0.8402 (mt0) REVERT: E 584 MET cc_start: 0.8729 (tpp) cc_final: 0.8439 (tpp) REVERT: E 620 GLU cc_start: 0.7605 (pt0) cc_final: 0.7198 (mp0) REVERT: E 713 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8423 (tp30) REVERT: E 765 GLU cc_start: 0.8040 (tp30) cc_final: 0.7719 (tp30) REVERT: E 772 ASP cc_start: 0.7843 (p0) cc_final: 0.7115 (p0) REVERT: E 778 ASP cc_start: 0.8848 (t0) cc_final: 0.8621 (t0) REVERT: E 999 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7461 (tpp80) REVERT: E 1001 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 1007 MET cc_start: 0.9189 (mmm) cc_final: 0.8777 (mmm) REVERT: F 55 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7138 (pp30) REVERT: F 57 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7801 (pt0) REVERT: F 61 GLU cc_start: 0.8431 (tp30) cc_final: 0.8106 (mm-30) REVERT: F 66 GLU cc_start: 0.6851 (mp0) cc_final: 0.6605 (mp0) REVERT: F 161 ASN cc_start: 0.7752 (m-40) cc_final: 0.7496 (m-40) REVERT: F 239 MET cc_start: 0.7563 (mmm) cc_final: 0.7004 (mmm) REVERT: F 299 LEU cc_start: 0.8927 (tp) cc_final: 0.8716 (pp) REVERT: F 677 ASN cc_start: 0.9231 (m110) cc_final: 0.9001 (m110) REVERT: G 31 HIS cc_start: 0.8444 (t70) cc_final: 0.8089 (p-80) REVERT: G 78 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7246 (tpt170) outliers start: 2 outliers final: 0 residues processed: 374 average time/residue: 0.3458 time to fit residues: 201.5649 Evaluate side-chains 305 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22701 Z= 0.169 Angle : 0.536 11.113 30716 Z= 0.271 Chirality : 0.042 0.194 3415 Planarity : 0.004 0.046 3898 Dihedral : 7.663 106.933 3189 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2673 helix: 1.78 (0.15), residues: 1239 sheet: -0.10 (0.37), residues: 228 loop : -1.00 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 322 HIS 0.007 0.001 HIS E 807 PHE 0.016 0.001 PHE G 52 TYR 0.025 0.001 TYR F 274 ARG 0.005 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASP cc_start: 0.9050 (t0) cc_final: 0.8838 (t0) REVERT: A 268 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 891 MET cc_start: 0.8954 (mtm) cc_final: 0.8708 (mtm) REVERT: A 921 MET cc_start: 0.8412 (tpp) cc_final: 0.8197 (tpp) REVERT: A 935 MET cc_start: 0.8550 (tmm) cc_final: 0.8126 (tmm) REVERT: B 49 LEU cc_start: 0.7552 (mt) cc_final: 0.7345 (mt) REVERT: B 57 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 163 LYS cc_start: 0.8364 (mttt) cc_final: 0.8117 (tttt) REVERT: B 239 MET cc_start: 0.3842 (tpp) cc_final: 0.1429 (tmm) REVERT: B 313 MET cc_start: 0.8358 (ptt) cc_final: 0.8048 (ppp) REVERT: B 382 TRP cc_start: 0.9353 (p-90) cc_final: 0.9044 (p90) REVERT: C 59 HIS cc_start: 0.8618 (m-70) cc_final: 0.8259 (m-70) REVERT: E 172 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8542 (mt-10) REVERT: E 197 GLN cc_start: 0.8799 (mt0) cc_final: 0.8415 (mt0) REVERT: E 233 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7920 (ttp80) REVERT: E 240 SER cc_start: 0.8507 (t) cc_final: 0.7487 (t) REVERT: E 252 ASP cc_start: 0.8760 (t0) cc_final: 0.8536 (t0) REVERT: E 398 ASP cc_start: 0.8615 (m-30) cc_final: 0.8365 (m-30) REVERT: E 406 MET cc_start: 0.9229 (mmp) cc_final: 0.8726 (mmp) REVERT: E 500 ASN cc_start: 0.8491 (t0) cc_final: 0.8202 (t0) REVERT: E 542 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8588 (mtmm) REVERT: E 550 GLN cc_start: 0.8686 (mt0) cc_final: 0.8396 (mt0) REVERT: E 584 MET cc_start: 0.8619 (tpp) cc_final: 0.8305 (tpp) REVERT: E 620 GLU cc_start: 0.7546 (pt0) cc_final: 0.7192 (mp0) REVERT: E 680 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7275 (tptp) REVERT: E 713 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8440 (tp30) REVERT: E 765 GLU cc_start: 0.8038 (tp30) cc_final: 0.7782 (tp30) REVERT: E 772 ASP cc_start: 0.7761 (p0) cc_final: 0.7047 (p0) REVERT: E 778 ASP cc_start: 0.8845 (t0) cc_final: 0.8617 (t0) REVERT: E 878 CYS cc_start: 0.8483 (m) cc_final: 0.8246 (m) REVERT: E 1001 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8080 (tm-30) REVERT: E 1007 MET cc_start: 0.9176 (mmm) cc_final: 0.8820 (mmm) REVERT: F 52 ARG cc_start: 0.7407 (mmm160) cc_final: 0.6320 (mtt90) REVERT: F 57 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8021 (pt0) REVERT: F 66 GLU cc_start: 0.6915 (mp0) cc_final: 0.6336 (mp0) REVERT: F 161 ASN cc_start: 0.7792 (m-40) cc_final: 0.7504 (m-40) REVERT: F 239 MET cc_start: 0.7625 (mmm) cc_final: 0.7195 (mmm) REVERT: F 399 PHE cc_start: 0.7876 (t80) cc_final: 0.7422 (t80) REVERT: F 677 ASN cc_start: 0.9210 (m110) cc_final: 0.8958 (m110) REVERT: F 678 MET cc_start: 0.8388 (mmp) cc_final: 0.8164 (tpp) REVERT: G 31 HIS cc_start: 0.8348 (t70) cc_final: 0.8012 (p-80) REVERT: G 78 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7275 (tpt170) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.3283 time to fit residues: 196.9497 Evaluate side-chains 306 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 147 optimal weight: 0.0980 chunk 219 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 810 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22701 Z= 0.290 Angle : 0.576 12.155 30716 Z= 0.291 Chirality : 0.043 0.239 3415 Planarity : 0.004 0.050 3898 Dihedral : 7.709 107.106 3189 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 1.12 % Favored : 98.84 % 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: 0.54 (0.17), residues: 2673 helix: 1.72 (0.15), residues: 1246 sheet: -0.21 (0.36), residues: 232 loop : -1.01 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 511 HIS 0.009 0.001 HIS A 807 PHE 0.016 0.002 PHE E 912 TYR 0.025 0.001 TYR C 76 ARG 0.006 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 MET cc_start: 0.9001 (mtm) cc_final: 0.8674 (mtm) REVERT: A 935 MET cc_start: 0.8559 (tmm) cc_final: 0.8118 (tmm) REVERT: B 57 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 163 LYS cc_start: 0.8380 (mttt) cc_final: 0.8119 (tttt) REVERT: B 239 MET cc_start: 0.3871 (tpp) cc_final: 0.1460 (tmm) REVERT: B 286 PHE cc_start: 0.7346 (m-80) cc_final: 0.7140 (m-80) REVERT: B 313 MET cc_start: 0.8365 (ptt) cc_final: 0.8039 (ppp) REVERT: B 318 TYR cc_start: 0.9017 (t80) cc_final: 0.8458 (t80) REVERT: B 382 TRP cc_start: 0.9368 (p-90) cc_final: 0.9089 (p90) REVERT: B 678 MET cc_start: 0.8645 (tpt) cc_final: 0.8437 (tpt) REVERT: C 59 HIS cc_start: 0.8609 (m-70) cc_final: 0.8149 (m-70) REVERT: E 172 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 240 SER cc_start: 0.8485 (t) cc_final: 0.7556 (t) REVERT: E 398 ASP cc_start: 0.8612 (m-30) cc_final: 0.8394 (m-30) REVERT: E 406 MET cc_start: 0.9249 (mmp) cc_final: 0.8626 (mmp) REVERT: E 500 ASN cc_start: 0.8555 (t0) cc_final: 0.8293 (t0) REVERT: E 542 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8538 (mtmm) REVERT: E 543 MET cc_start: 0.9074 (tpt) cc_final: 0.8815 (tpt) REVERT: E 550 GLN cc_start: 0.8687 (mt0) cc_final: 0.8402 (mt0) REVERT: E 584 MET cc_start: 0.8698 (tpp) cc_final: 0.8388 (tpp) REVERT: E 620 GLU cc_start: 0.7650 (pt0) cc_final: 0.7272 (mp0) REVERT: E 680 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7308 (tptp) REVERT: E 713 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8448 (tp30) REVERT: E 765 GLU cc_start: 0.8078 (tp30) cc_final: 0.7758 (tp30) REVERT: E 772 ASP cc_start: 0.7844 (p0) cc_final: 0.7185 (p0) REVERT: E 778 ASP cc_start: 0.8881 (t0) cc_final: 0.8665 (t0) REVERT: E 878 CYS cc_start: 0.8401 (m) cc_final: 0.8197 (m) REVERT: E 1001 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8117 (tm-30) REVERT: E 1007 MET cc_start: 0.9201 (mmm) cc_final: 0.8853 (mmm) REVERT: F 57 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7951 (pt0) REVERT: F 66 GLU cc_start: 0.6815 (mp0) cc_final: 0.6169 (mp0) REVERT: F 161 ASN cc_start: 0.7753 (m-40) cc_final: 0.7470 (m-40) REVERT: F 239 MET cc_start: 0.7626 (mmm) cc_final: 0.7201 (mmm) REVERT: F 677 ASN cc_start: 0.9186 (m110) cc_final: 0.8913 (m110) REVERT: G 31 HIS cc_start: 0.8450 (t70) cc_final: 0.8084 (p-80) REVERT: G 78 ARG cc_start: 0.7824 (ttt180) cc_final: 0.7267 (tpt170) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.3213 time to fit residues: 183.2070 Evaluate side-chains 293 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 22701 Z= 0.302 Angle : 0.581 11.136 30716 Z= 0.294 Chirality : 0.043 0.263 3415 Planarity : 0.004 0.053 3898 Dihedral : 7.737 106.646 3189 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2673 helix: 1.69 (0.15), residues: 1246 sheet: -0.23 (0.36), residues: 232 loop : -1.03 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 322 HIS 0.005 0.001 HIS F 109 PHE 0.016 0.002 PHE B 286 TYR 0.027 0.001 TYR F 274 ARG 0.005 0.000 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 921 MET cc_start: 0.8483 (tpp) cc_final: 0.8122 (tpp) REVERT: A 935 MET cc_start: 0.8502 (tmm) cc_final: 0.8162 (tmm) REVERT: B 57 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 163 LYS cc_start: 0.8401 (mttt) cc_final: 0.8124 (tttt) REVERT: B 239 MET cc_start: 0.3967 (tpp) cc_final: 0.1558 (tmm) REVERT: B 313 MET cc_start: 0.8369 (ptt) cc_final: 0.8083 (ppp) REVERT: B 318 TYR cc_start: 0.9014 (t80) cc_final: 0.8434 (t80) REVERT: B 382 TRP cc_start: 0.9372 (p-90) cc_final: 0.9127 (p90) REVERT: B 678 MET cc_start: 0.8645 (tpt) cc_final: 0.8413 (tpt) REVERT: C 59 HIS cc_start: 0.8605 (m-70) cc_final: 0.8143 (m-70) REVERT: E 172 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8592 (mt-10) REVERT: E 240 SER cc_start: 0.8584 (t) cc_final: 0.7591 (t) REVERT: E 252 ASP cc_start: 0.8798 (t0) cc_final: 0.8574 (t0) REVERT: E 259 ASP cc_start: 0.8837 (t70) cc_final: 0.8603 (t70) REVERT: E 398 ASP cc_start: 0.8616 (m-30) cc_final: 0.8391 (m-30) REVERT: E 406 MET cc_start: 0.9252 (mmp) cc_final: 0.8652 (mmp) REVERT: E 500 ASN cc_start: 0.8582 (t0) cc_final: 0.8293 (t0) REVERT: E 542 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8578 (mtmm) REVERT: E 550 GLN cc_start: 0.8678 (mt0) cc_final: 0.8401 (mt0) REVERT: E 584 MET cc_start: 0.8754 (tpp) cc_final: 0.8393 (tpp) REVERT: E 620 GLU cc_start: 0.7558 (pt0) cc_final: 0.7198 (mp0) REVERT: E 680 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7304 (tptp) REVERT: E 713 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8453 (tp30) REVERT: E 765 GLU cc_start: 0.8051 (tp30) cc_final: 0.7716 (tp30) REVERT: E 772 ASP cc_start: 0.7850 (p0) cc_final: 0.7195 (p0) REVERT: E 778 ASP cc_start: 0.8879 (t0) cc_final: 0.8664 (t0) REVERT: E 879 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8049 (tt0) REVERT: E 1001 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8046 (tm-30) REVERT: E 1007 MET cc_start: 0.9206 (mmm) cc_final: 0.8837 (mmm) REVERT: F 57 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7957 (pt0) REVERT: F 66 GLU cc_start: 0.6752 (mp0) cc_final: 0.5942 (mp0) REVERT: F 161 ASN cc_start: 0.7754 (m-40) cc_final: 0.7469 (m-40) REVERT: F 239 MET cc_start: 0.7624 (mmm) cc_final: 0.7182 (mmm) REVERT: G 31 HIS cc_start: 0.8459 (t70) cc_final: 0.8091 (p-80) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.3272 time to fit residues: 184.1889 Evaluate side-chains 295 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 0.0050 chunk 249 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 241 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22701 Z= 0.183 Angle : 0.550 10.985 30716 Z= 0.278 Chirality : 0.042 0.268 3415 Planarity : 0.004 0.047 3898 Dihedral : 7.618 105.972 3189 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.04 % Allowed : 0.62 % Favored : 99.34 % 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: 0.56 (0.17), residues: 2673 helix: 1.72 (0.15), residues: 1244 sheet: -0.09 (0.36), residues: 228 loop : -1.01 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 322 HIS 0.004 0.001 HIS E 807 PHE 0.022 0.001 PHE E 912 TYR 0.016 0.001 TYR C 76 ARG 0.004 0.000 ARG E 999 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.565 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 252 ASP cc_start: 0.9032 (t0) cc_final: 0.8814 (t0) REVERT: A 921 MET cc_start: 0.8433 (tpp) cc_final: 0.8155 (tpp) REVERT: A 935 MET cc_start: 0.8494 (tmm) cc_final: 0.8153 (tmm) REVERT: B 57 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 163 LYS cc_start: 0.8367 (mttt) cc_final: 0.8101 (tttt) REVERT: B 239 MET cc_start: 0.4036 (tpp) cc_final: 0.1694 (tmm) REVERT: B 313 MET cc_start: 0.8385 (ptt) cc_final: 0.8116 (ppp) REVERT: B 318 TYR cc_start: 0.8998 (t80) cc_final: 0.8357 (t80) REVERT: B 382 TRP cc_start: 0.9352 (p-90) cc_final: 0.9090 (p90) REVERT: B 390 MET cc_start: 0.7290 (mmm) cc_final: 0.6917 (mmm) REVERT: B 678 MET cc_start: 0.8622 (tpt) cc_final: 0.8409 (tpt) REVERT: C 59 HIS cc_start: 0.8610 (m-70) cc_final: 0.8154 (m-70) REVERT: E 172 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8564 (mt-10) REVERT: E 240 SER cc_start: 0.8561 (t) cc_final: 0.7395 (t) REVERT: E 252 ASP cc_start: 0.8782 (t0) cc_final: 0.8572 (t0) REVERT: E 398 ASP cc_start: 0.8587 (m-30) cc_final: 0.8357 (m-30) REVERT: E 406 MET cc_start: 0.9234 (mmp) cc_final: 0.8793 (mmp) REVERT: E 500 ASN cc_start: 0.8476 (t0) cc_final: 0.8239 (t0) REVERT: E 542 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8535 (mtmm) REVERT: E 550 GLN cc_start: 0.8664 (mt0) cc_final: 0.8439 (mt0) REVERT: E 584 MET cc_start: 0.8671 (tpp) cc_final: 0.8268 (tpp) REVERT: E 620 GLU cc_start: 0.7490 (pt0) cc_final: 0.7173 (mp0) REVERT: E 680 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7286 (tptp) REVERT: E 713 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8408 (tp30) REVERT: E 765 GLU cc_start: 0.7993 (tp30) cc_final: 0.7741 (tp30) REVERT: E 772 ASP cc_start: 0.7780 (p0) cc_final: 0.7070 (p0) REVERT: E 778 ASP cc_start: 0.8861 (t0) cc_final: 0.8650 (t0) REVERT: E 878 CYS cc_start: 0.8486 (m) cc_final: 0.8277 (m) REVERT: E 879 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7897 (tt0) REVERT: F 52 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6421 (mtt90) REVERT: F 57 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7955 (pt0) REVERT: F 66 GLU cc_start: 0.6790 (mp0) cc_final: 0.6406 (mp0) REVERT: F 161 ASN cc_start: 0.7776 (m-40) cc_final: 0.7480 (m-40) REVERT: F 163 LYS cc_start: 0.8475 (tttm) cc_final: 0.8261 (tttm) REVERT: F 239 MET cc_start: 0.7588 (mmm) cc_final: 0.7153 (mmm) REVERT: F 295 LEU cc_start: 0.8324 (tp) cc_final: 0.8074 (tp) REVERT: G 31 HIS cc_start: 0.8408 (t70) cc_final: 0.8029 (p-80) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3351 time to fit residues: 190.5084 Evaluate side-chains 300 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 165 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22701 Z= 0.215 Angle : 0.558 10.783 30716 Z= 0.282 Chirality : 0.042 0.274 3415 Planarity : 0.004 0.047 3898 Dihedral : 7.601 106.241 3189 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % 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: 0.54 (0.17), residues: 2673 helix: 1.70 (0.15), residues: 1246 sheet: -0.07 (0.35), residues: 228 loop : -1.03 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 322 HIS 0.005 0.001 HIS E 807 PHE 0.018 0.001 PHE E 912 TYR 0.027 0.001 TYR F 274 ARG 0.006 0.000 ARG E 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.796 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 252 ASP cc_start: 0.9020 (t0) cc_final: 0.8808 (t0) REVERT: A 891 MET cc_start: 0.9045 (mtt) cc_final: 0.8828 (mtm) REVERT: A 921 MET cc_start: 0.8432 (tpp) cc_final: 0.8160 (tpp) REVERT: A 935 MET cc_start: 0.8376 (tmm) cc_final: 0.8085 (tmm) REVERT: B 57 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 163 LYS cc_start: 0.8374 (mttt) cc_final: 0.8109 (tttt) REVERT: B 239 MET cc_start: 0.4031 (tpp) cc_final: 0.1679 (tmm) REVERT: B 313 MET cc_start: 0.8463 (ptt) cc_final: 0.8080 (ppp) REVERT: B 318 TYR cc_start: 0.9012 (t80) cc_final: 0.8455 (t80) REVERT: B 359 TYR cc_start: 0.8300 (m-10) cc_final: 0.7899 (m-10) REVERT: B 382 TRP cc_start: 0.9358 (p-90) cc_final: 0.9105 (p90) REVERT: B 390 MET cc_start: 0.7420 (mmm) cc_final: 0.7078 (mmm) REVERT: C 59 HIS cc_start: 0.8595 (m-70) cc_final: 0.8124 (m-70) REVERT: C 74 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7773 (tptt) REVERT: E 172 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8568 (mt-10) REVERT: E 240 SER cc_start: 0.8611 (t) cc_final: 0.7329 (t) REVERT: E 398 ASP cc_start: 0.8587 (m-30) cc_final: 0.8356 (m-30) REVERT: E 406 MET cc_start: 0.9214 (mmp) cc_final: 0.8751 (mmp) REVERT: E 500 ASN cc_start: 0.8520 (t0) cc_final: 0.8274 (t0) REVERT: E 542 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8546 (mtmm) REVERT: E 550 GLN cc_start: 0.8653 (mt0) cc_final: 0.8434 (mt0) REVERT: E 584 MET cc_start: 0.8682 (tpp) cc_final: 0.8300 (tpp) REVERT: E 620 GLU cc_start: 0.7476 (pt0) cc_final: 0.7188 (mp0) REVERT: E 680 LYS cc_start: 0.7663 (tmtt) cc_final: 0.7246 (tptp) REVERT: E 713 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8480 (tp30) REVERT: E 765 GLU cc_start: 0.7995 (tp30) cc_final: 0.7685 (tp30) REVERT: E 772 ASP cc_start: 0.7779 (p0) cc_final: 0.7078 (p0) REVERT: E 778 ASP cc_start: 0.8867 (t0) cc_final: 0.8660 (t0) REVERT: E 878 CYS cc_start: 0.8599 (m) cc_final: 0.8256 (m) REVERT: E 879 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7918 (tt0) REVERT: E 967 MET cc_start: 0.8928 (mtp) cc_final: 0.8429 (mtp) REVERT: F 52 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6418 (mtt90) REVERT: F 57 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7870 (pt0) REVERT: F 66 GLU cc_start: 0.6797 (mp0) cc_final: 0.6189 (mp0) REVERT: F 133 LYS cc_start: 0.5554 (tttt) cc_final: 0.5162 (mmtm) REVERT: F 161 ASN cc_start: 0.7780 (m-40) cc_final: 0.7482 (m-40) REVERT: F 163 LYS cc_start: 0.8474 (tttm) cc_final: 0.8273 (tttm) REVERT: F 239 MET cc_start: 0.7585 (mmm) cc_final: 0.7142 (mmm) REVERT: F 299 LEU cc_start: 0.8736 (tp) cc_final: 0.8501 (pp) REVERT: F 390 MET cc_start: 0.3497 (ttt) cc_final: 0.1252 (tmm) REVERT: F 399 PHE cc_start: 0.7843 (t80) cc_final: 0.7467 (t80) REVERT: G 31 HIS cc_start: 0.8423 (t70) cc_final: 0.8009 (p-80) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.3254 time to fit residues: 181.8120 Evaluate side-chains 294 residues out of total 2409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 197 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN F 126 GLN G 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090956 restraints weight = 48985.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.090066 restraints weight = 46973.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091005 restraints weight = 47568.630| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22701 Z= 0.201 Angle : 0.551 10.837 30716 Z= 0.278 Chirality : 0.042 0.267 3415 Planarity : 0.004 0.046 3898 Dihedral : 7.549 105.882 3189 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2673 helix: 1.70 (0.15), residues: 1243 sheet: 0.07 (0.36), residues: 218 loop : -1.06 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 322 HIS 0.004 0.001 HIS E 807 PHE 0.020 0.001 PHE E 912 TYR 0.015 0.001 TYR E 643 ARG 0.006 0.000 ARG G 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.71 seconds wall clock time: 82 minutes 3.46 seconds (4923.46 seconds total)