Starting phenix.real_space_refine on Wed Feb 14 16:23:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btf_30178/02_2024/7btf_30178.pdb" } resolution = 2.95 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= 0.002 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 72 5.16 5 C 6169 2.51 5 N 1623 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 761": "OD1" <-> "OD2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9685 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7376 Classifications: {'peptide': 915} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 884} Chain breaks: 1 Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 519 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 77.360 41.287 55.906 1.00 42.50 S ATOM 2487 SG CYS A 306 78.109 43.610 52.156 1.00 41.35 S ATOM 2519 SG CYS A 310 74.348 41.738 52.526 1.00 38.79 S ATOM 3927 SG CYS A 487 87.475 47.957 72.323 1.00 45.06 S ATOM 5180 SG CYS A 645 89.713 50.141 69.110 1.00 51.29 S ATOM 5186 SG CYS A 646 87.594 46.201 68.845 1.00 47.12 S Time building chain proxies: 5.68, per 1000 atoms: 0.59 Number of scatterers: 9685 At special positions: 0 Unit cell: (110.7, 103.32, 131.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 72 16.00 O 1819 8.00 N 1623 7.00 C 6169 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: 3.87 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 48.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 4.091A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.159A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.351A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.758A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.724A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.356A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.083A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.086A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.108A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.889A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.812A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.730A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.754A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.743A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.720A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.841A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.930A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.134A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.962A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.660A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.046A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.926A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.041A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.097A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.479A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.760A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 149 " --> pdb=" O ALA D 152 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 4.22 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: 3131 1.34 - 1.46: 1963 1.46 - 1.57: 4695 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 9898 Sorted by residual: bond pdb=" CG LEU A 731 " pdb=" CD2 LEU A 731 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB VAL A 605 " pdb=" CG2 VAL A 605 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" C LEU A 329 " pdb=" N VAL A 330 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.08e-02 2.31e+03 2.43e+00 bond pdb=" CB ARG A 116 " pdb=" CG ARG A 116 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CA TYR A 606 " pdb=" C TYR A 606 " ideal model delta sigma weight residual 1.518 1.460 0.058 4.01e-02 6.22e+02 2.08e+00 ... (remaining 9893 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.12: 178 106.12 - 113.10: 5387 113.10 - 120.08: 3623 120.08 - 127.07: 4155 127.07 - 134.05: 95 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N TRP B 182 " pdb=" CA TRP B 182 " pdb=" C TRP B 182 " ideal model delta sigma weight residual 109.81 122.48 -12.67 2.21e+00 2.05e-01 3.29e+01 angle pdb=" CA TRP B 182 " pdb=" CB TRP B 182 " pdb=" CG TRP B 182 " ideal model delta sigma weight residual 113.60 105.63 7.97 1.90e+00 2.77e-01 1.76e+01 angle pdb=" N THR A 20 " pdb=" CA THR A 20 " pdb=" C THR A 20 " ideal model delta sigma weight residual 109.83 104.89 4.94 1.27e+00 6.20e-01 1.51e+01 angle pdb=" N VAL A 588 " pdb=" CA VAL A 588 " pdb=" C VAL A 588 " ideal model delta sigma weight residual 106.21 110.19 -3.98 1.07e+00 8.73e-01 1.38e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 117.79 -7.98 2.21e+00 2.05e-01 1.31e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5430 17.75 - 35.50: 399 35.50 - 53.25: 58 53.25 - 71.00: 8 71.00 - 88.75: 9 Dihedral angle restraints: 5904 sinusoidal: 2305 harmonic: 3599 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ALA B 181 " pdb=" C ALA B 181 " pdb=" N TRP B 182 " pdb=" CA TRP B 182 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA D 181 " pdb=" C ALA D 181 " pdb=" N TRP D 182 " pdb=" CA TRP D 182 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 5901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1387 0.087 - 0.175: 125 0.175 - 0.262: 2 0.262 - 0.349: 0 0.349 - 0.436: 1 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA TRP D 182 " pdb=" N TRP D 182 " pdb=" C TRP D 182 " pdb=" CB TRP D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 588 " pdb=" CA VAL A 588 " pdb=" CG1 VAL A 588 " pdb=" CG2 VAL A 588 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 1512 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO D 183 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 182 " 0.021 2.00e-02 2.50e+03 1.48e-02 5.45e+00 pdb=" CG TRP B 182 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 182 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 182 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 182 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 182 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 182 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 182 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 182 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 182 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C LEU A 302 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 302 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 303 " -0.013 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2466 2.79 - 3.32: 8758 3.32 - 3.84: 15542 3.84 - 4.37: 19069 4.37 - 4.90: 33014 Nonbonded interactions: 78849 Sorted by model distance: nonbonded pdb=" OD1 ASP A 194 " pdb=" OH TYR A 289 " model vdw 2.262 2.440 nonbonded pdb=" O ASP A 235 " pdb=" OG SER A 239 " model vdw 2.290 2.440 nonbonded pdb=" O SER B 76 " pdb=" N LYS B 79 " model vdw 2.296 2.520 nonbonded pdb=" OD1 ASP A 164 " pdb=" N PHE A 165 " model vdw 2.317 2.520 nonbonded pdb=" OG SER A 343 " pdb=" OD1 ASP A 377 " model vdw 2.349 2.440 ... (remaining 78844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.830 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.510 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.009 0.061 9898 Z= 0.574 Angle : 0.726 12.674 13438 Z= 0.408 Chirality : 0.052 0.436 1515 Planarity : 0.004 0.060 1718 Dihedral : 12.871 88.750 3576 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1201 helix: -1.20 (0.19), residues: 526 sheet: -1.53 (0.40), residues: 134 loop : -2.77 (0.22), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.002 PHE A 753 TYR 0.019 0.002 TYR A 80 ARG 0.005 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 780 LYS cc_start: 0.8202 (pttt) cc_final: 0.7852 (pttp) REVERT: B 164 SER cc_start: 0.9011 (m) cc_final: 0.8733 (p) REVERT: D 90 MET cc_start: 0.7881 (ttm) cc_final: 0.7664 (ttp) REVERT: D 96 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7381 (ttp-170) REVERT: D 161 ASP cc_start: 0.7537 (p0) cc_final: 0.6686 (t0) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 1.2955 time to fit residues: 197.9877 Evaluate side-chains 106 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 209 ASN A 312 ASN A 356 ASN A 414 ASN A 573 GLN A 611 ASN A 613 HIS A 713 ASN A 773 GLN A 790 ASN C 36 HIS B 118 ASN D 105 ASN D 157 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9898 Z= 0.157 Angle : 0.522 9.957 13438 Z= 0.275 Chirality : 0.042 0.261 1515 Planarity : 0.004 0.051 1718 Dihedral : 4.673 28.005 1325 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.61 % Allowed : 9.50 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1201 helix: 0.04 (0.22), residues: 531 sheet: -0.95 (0.41), residues: 144 loop : -2.12 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.011 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.010 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.125 Fit side-chains REVERT: B 164 SER cc_start: 0.8958 (m) cc_final: 0.8730 (p) REVERT: D 96 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7416 (ttp-170) REVERT: D 161 ASP cc_start: 0.7396 (p0) cc_final: 0.6689 (t0) outliers start: 28 outliers final: 9 residues processed: 131 average time/residue: 1.2565 time to fit residues: 177.0847 Evaluate side-chains 113 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.3980 chunk 33 optimal weight: 0.0170 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9898 Z= 0.222 Angle : 0.522 8.768 13438 Z= 0.274 Chirality : 0.043 0.251 1515 Planarity : 0.003 0.056 1718 Dihedral : 4.505 27.815 1323 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.98 % Allowed : 11.36 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.99 (0.24), residues: 1201 helix: 0.45 (0.23), residues: 533 sheet: -0.62 (0.44), residues: 131 loop : -1.82 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.140 Fit side-chains REVERT: A 105 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7159 (ttp80) REVERT: A 160 LYS cc_start: 0.7715 (tppt) cc_final: 0.7376 (tttm) REVERT: A 252 THR cc_start: 0.8923 (t) cc_final: 0.8658 (m) REVERT: A 726 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6821 (mtp85) REVERT: B 164 SER cc_start: 0.8941 (m) cc_final: 0.8706 (p) REVERT: D 96 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7443 (ttp-170) REVERT: D 161 ASP cc_start: 0.7269 (p0) cc_final: 0.6636 (t0) outliers start: 32 outliers final: 14 residues processed: 131 average time/residue: 1.2663 time to fit residues: 177.7952 Evaluate side-chains 120 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 102 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN A 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9898 Z= 0.285 Angle : 0.550 8.271 13438 Z= 0.289 Chirality : 0.045 0.254 1515 Planarity : 0.004 0.057 1718 Dihedral : 4.577 27.730 1323 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.98 % Allowed : 12.66 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1201 helix: 0.54 (0.23), residues: 537 sheet: -0.48 (0.44), residues: 131 loop : -1.70 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.012 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.162 Fit side-chains REVERT: A 105 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7211 (ttp80) REVERT: A 160 LYS cc_start: 0.7799 (tppt) cc_final: 0.7464 (tttm) REVERT: A 252 THR cc_start: 0.8934 (t) cc_final: 0.8658 (m) REVERT: A 726 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6783 (mtp85) REVERT: B 164 SER cc_start: 0.8958 (m) cc_final: 0.8714 (p) REVERT: D 96 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7430 (ttp-170) REVERT: D 161 ASP cc_start: 0.7286 (p0) cc_final: 0.6631 (t0) outliers start: 32 outliers final: 17 residues processed: 122 average time/residue: 1.4144 time to fit residues: 184.2917 Evaluate side-chains 118 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 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 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9898 Z= 0.198 Angle : 0.501 7.639 13438 Z= 0.264 Chirality : 0.043 0.225 1515 Planarity : 0.003 0.054 1718 Dihedral : 4.358 25.868 1323 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.35 % Allowed : 13.31 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1201 helix: 0.74 (0.23), residues: 542 sheet: -0.40 (0.44), residues: 131 loop : -1.57 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.012 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7204 (ttp80) REVERT: A 160 LYS cc_start: 0.7792 (tppt) cc_final: 0.7496 (tttm) REVERT: A 365 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7397 (tpm170) REVERT: A 726 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6774 (mtp85) REVERT: A 894 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7269 (pp20) REVERT: D 96 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7399 (ttp-170) REVERT: D 161 ASP cc_start: 0.7257 (p0) cc_final: 0.6679 (t0) outliers start: 36 outliers final: 12 residues processed: 124 average time/residue: 1.3357 time to fit residues: 178.4163 Evaluate side-chains 111 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9898 Z= 0.205 Angle : 0.505 7.575 13438 Z= 0.266 Chirality : 0.043 0.222 1515 Planarity : 0.004 0.075 1718 Dihedral : 4.325 25.711 1323 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.70 % Allowed : 14.06 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.41 (0.24), residues: 1201 helix: 0.86 (0.23), residues: 542 sheet: -0.30 (0.44), residues: 131 loop : -1.46 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.016 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7221 (ttp80) REVERT: A 160 LYS cc_start: 0.7732 (tppt) cc_final: 0.7446 (tttm) REVERT: A 252 THR cc_start: 0.8948 (t) cc_final: 0.8650 (m) REVERT: A 365 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7379 (tpm170) REVERT: A 726 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: D 96 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7414 (ttp-170) REVERT: D 161 ASP cc_start: 0.7221 (p0) cc_final: 0.6677 (t0) outliers start: 29 outliers final: 17 residues processed: 122 average time/residue: 1.2931 time to fit residues: 169.1687 Evaluate side-chains 117 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 71 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN D 105 ASN D 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9898 Z= 0.246 Angle : 0.516 7.898 13438 Z= 0.272 Chirality : 0.044 0.233 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.370 25.784 1323 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.35 % Allowed : 14.25 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1201 helix: 0.86 (0.23), residues: 538 sheet: -0.29 (0.44), residues: 131 loop : -1.44 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.008 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7241 (ttp80) REVERT: A 160 LYS cc_start: 0.7762 (tppt) cc_final: 0.7480 (tttm) REVERT: A 252 THR cc_start: 0.8942 (t) cc_final: 0.8635 (m) REVERT: A 726 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6765 (mtp85) REVERT: D 96 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7413 (ttp-170) REVERT: D 161 ASP cc_start: 0.7265 (p0) cc_final: 0.6661 (t0) REVERT: D 174 MET cc_start: 0.2988 (mtm) cc_final: 0.2673 (ppp) outliers start: 36 outliers final: 19 residues processed: 126 average time/residue: 1.2267 time to fit residues: 165.7737 Evaluate side-chains 119 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9898 Z= 0.317 Angle : 0.549 8.491 13438 Z= 0.288 Chirality : 0.045 0.246 1515 Planarity : 0.004 0.083 1718 Dihedral : 4.503 26.902 1323 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.98 % Allowed : 15.55 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.44 (0.24), residues: 1201 helix: 0.84 (0.23), residues: 531 sheet: -0.27 (0.44), residues: 131 loop : -1.46 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.002 PHE A 741 TYR 0.016 0.001 TYR A 788 ARG 0.018 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7275 (ttp80) REVERT: A 116 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7356 (mtt180) REVERT: A 160 LYS cc_start: 0.7768 (tppt) cc_final: 0.7466 (tttm) REVERT: A 252 THR cc_start: 0.8957 (t) cc_final: 0.8645 (m) REVERT: A 726 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6768 (mtp85) REVERT: A 780 LYS cc_start: 0.8059 (pttt) cc_final: 0.7759 (pttp) REVERT: D 96 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7420 (ttp-170) REVERT: D 161 ASP cc_start: 0.7298 (p0) cc_final: 0.6643 (t0) outliers start: 32 outliers final: 23 residues processed: 120 average time/residue: 1.3677 time to fit residues: 175.3994 Evaluate side-chains 124 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9898 Z= 0.243 Angle : 0.522 9.006 13438 Z= 0.274 Chirality : 0.044 0.231 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.406 25.719 1323 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.89 % Allowed : 15.46 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.37 (0.24), residues: 1201 helix: 0.88 (0.24), residues: 532 sheet: -0.25 (0.45), residues: 131 loop : -1.40 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.015 0.001 TYR A 831 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: A 116 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: A 160 LYS cc_start: 0.7739 (tppt) cc_final: 0.7446 (tttm) REVERT: A 252 THR cc_start: 0.8968 (t) cc_final: 0.8649 (m) REVERT: A 726 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: D 96 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7412 (ttp-170) REVERT: D 97 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7818 (pttt) REVERT: D 161 ASP cc_start: 0.7268 (p0) cc_final: 0.6607 (t0) REVERT: D 174 MET cc_start: 0.2929 (mtm) cc_final: 0.2686 (ppp) outliers start: 31 outliers final: 21 residues processed: 121 average time/residue: 1.3326 time to fit residues: 174.0806 Evaluate side-chains 119 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9898 Z= 0.186 Angle : 0.501 9.412 13438 Z= 0.263 Chirality : 0.043 0.213 1515 Planarity : 0.003 0.054 1718 Dihedral : 4.265 24.774 1323 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.61 % Allowed : 16.20 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.24), residues: 1201 helix: 0.91 (0.24), residues: 543 sheet: -0.26 (0.44), residues: 131 loop : -1.34 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.012 0.001 PHE A 741 TYR 0.014 0.001 TYR A 831 ARG 0.004 0.000 ARG A 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.7758 (tppt) cc_final: 0.7471 (tttm) REVERT: A 252 THR cc_start: 0.8952 (t) cc_final: 0.8642 (m) REVERT: A 726 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6767 (mtp85) REVERT: D 96 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7403 (ttp-170) REVERT: D 161 ASP cc_start: 0.7214 (p0) cc_final: 0.6636 (t0) REVERT: D 174 MET cc_start: 0.2807 (mtm) cc_final: 0.2589 (ppp) outliers start: 28 outliers final: 18 residues processed: 120 average time/residue: 1.3826 time to fit residues: 177.3201 Evaluate side-chains 119 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN C 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091351 restraints weight = 13636.817| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.76 r_work: 0.2985 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9898 Z= 0.268 Angle : 0.546 10.220 13438 Z= 0.286 Chirality : 0.044 0.232 1515 Planarity : 0.004 0.086 1718 Dihedral : 4.401 25.509 1323 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.33 % Allowed : 16.85 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.33 (0.24), residues: 1201 helix: 0.86 (0.23), residues: 538 sheet: -0.19 (0.45), residues: 131 loop : -1.36 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.017 0.001 TYR A 831 ARG 0.019 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3551.85 seconds wall clock time: 63 minutes 59.88 seconds (3839.88 seconds total)