Starting phenix.real_space_refine on Fri Nov 15 20:21:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jkb_61550/11_2024/9jkb_61550.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6063 2.51 5 N 1602 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9532 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1343 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 6015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 6015 Classifications: {'peptide': 736} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 722} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1257 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 86} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 9.19, per 1000 atoms: 0.96 Number of scatterers: 9532 At special positions: 0 Unit cell: (82, 115.62, 181.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1819 8.00 N 1602 7.00 C 6063 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 - 3.00 Amino acid : True - 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 64.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.941A pdb=" N SER C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.968A pdb=" N LYS C 281 " --> pdb=" O PRO C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 314 Processing helix chain 'C' and resid 315 through 319 removed outlier: 3.681A pdb=" N GLY C 319 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.843A pdb=" N LEU C 352 " --> pdb=" O HIS C 349 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 354 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.620A pdb=" N ILE C 377 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 33 removed outlier: 4.348A pdb=" N ASP A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 85 through 107 removed outlier: 3.574A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.670A pdb=" N LEU A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.543A pdb=" N LEU A 171 " --> pdb=" O TRP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 4.820A pdb=" N LYS A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.276A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 232 through 255 Processing helix chain 'A' and resid 256 through 279 removed outlier: 3.583A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.310A pdb=" N GLU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.781A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.439A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.774A pdb=" N TYR A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.783A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 416 through 429 removed outlier: 3.526A pdb=" N GLU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.579A pdb=" N PHE A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 497 removed outlier: 3.503A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.634A pdb=" N SER A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 632 through 647 Processing helix chain 'A' and resid 688 through 723 removed outlier: 3.533A pdb=" N LYS A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 739 Processing helix chain 'A' and resid 745 through 758 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 24 through 33 Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.813A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.743A pdb=" N PHE D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.556A pdb=" N CYS D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN D 81 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 4.256A pdb=" N GLU D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'D' and resid 138 through 147 Processing sheet with id=AA1, first strand: chain 'C' and resid 234 through 235 removed outlier: 3.574A pdb=" N SER C 329 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 331 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.623A pdb=" N GLN A 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRP R 33 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TRP R 35 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 589 removed outlier: 3.557A pdb=" N GLY A 588 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 603 " --> pdb=" O GLY A 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 621 removed outlier: 3.513A pdb=" N VAL A 650 " --> pdb=" O LYS A 670 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 763 through 764 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 4 529 hydrogen bonds defined for protein. 1554 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: 2.78 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3127 1.34 - 1.46: 1914 1.46 - 1.58: 4600 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 9716 Sorted by residual: bond pdb=" C LYS D 126 " pdb=" N PRO D 127 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.11e-02 8.12e+03 1.29e+01 bond pdb=" N ASN D 86 " pdb=" CA ASN D 86 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.45e+00 bond pdb=" C VAL A 746 " pdb=" N PRO A 747 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.15e+00 bond pdb=" N ASN B 140 " pdb=" CA ASN B 140 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.42e-02 4.96e+03 9.56e-01 bond pdb=" CA LYS D 126 " pdb=" C LYS D 126 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.21e-01 ... (remaining 9711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 13016 2.85 - 5.70: 99 5.70 - 8.56: 13 8.56 - 11.41: 2 11.41 - 14.26: 2 Bond angle restraints: 13132 Sorted by residual: angle pdb=" CA LEU C 367 " pdb=" CB LEU C 367 " pdb=" CG LEU C 367 " ideal model delta sigma weight residual 116.30 130.56 -14.26 3.50e+00 8.16e-02 1.66e+01 angle pdb=" C ARG A 401 " pdb=" N PHE A 402 " pdb=" CA PHE A 402 " ideal model delta sigma weight residual 122.54 116.16 6.38 1.65e+00 3.67e-01 1.49e+01 angle pdb=" CA LEU D 121 " pdb=" CB LEU D 121 " pdb=" CG LEU D 121 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" C GLN B 90 " pdb=" N GLU B 91 " pdb=" CA GLU B 91 " ideal model delta sigma weight residual 121.58 114.46 7.12 1.95e+00 2.63e-01 1.33e+01 angle pdb=" CA TYR A 570 " pdb=" CB TYR A 570 " pdb=" CG TYR A 570 " ideal model delta sigma weight residual 113.90 120.16 -6.26 1.80e+00 3.09e-01 1.21e+01 ... (remaining 13127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5165 17.66 - 35.32: 601 35.32 - 52.98: 114 52.98 - 70.64: 21 70.64 - 88.30: 13 Dihedral angle restraints: 5914 sinusoidal: 2431 harmonic: 3483 Sorted by residual: dihedral pdb=" CA ILE A 20 " pdb=" C ILE A 20 " pdb=" N TRP A 21 " pdb=" CA TRP A 21 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLU A 758 " pdb=" C GLU A 758 " pdb=" N LYS A 759 " pdb=" CA LYS A 759 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA CYS A 137 " pdb=" C CYS A 137 " pdb=" N ALA A 138 " pdb=" CA ALA A 138 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 959 0.035 - 0.071: 349 0.071 - 0.106: 113 0.106 - 0.142: 40 0.142 - 0.177: 5 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA GLU A 758 " pdb=" N GLU A 758 " pdb=" C GLU A 758 " pdb=" CB GLU A 758 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB VAL B 25 " pdb=" CA VAL B 25 " pdb=" CG1 VAL B 25 " pdb=" CG2 VAL B 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1463 not shown) Planarity restraints: 1685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 136 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C ILE A 136 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE A 136 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A 137 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 124 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C GLU A 124 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 124 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 125 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 119 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C TYR A 119 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR A 119 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 120 " -0.014 2.00e-02 2.50e+03 ... (remaining 1682 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2176 2.78 - 3.31: 9744 3.31 - 3.84: 16636 3.84 - 4.37: 18090 4.37 - 4.90: 30594 Nonbonded interactions: 77240 Sorted by model distance: nonbonded pdb=" OH TYR A 260 " pdb=" O LEU A 295 " model vdw 2.253 3.040 nonbonded pdb=" O GLY A 212 " pdb=" OG1 THR A 224 " model vdw 2.266 3.040 nonbonded pdb=" O ILE C 310 " pdb=" OG1 THR C 314 " model vdw 2.271 3.040 nonbonded pdb=" O CYS D 80 " pdb=" OG SER D 84 " model vdw 2.296 3.040 nonbonded pdb=" OG SER A 514 " pdb=" O VAL A 539 " model vdw 2.297 3.040 ... (remaining 77235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 7.860 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.003 0.040 9716 Z= 0.211 Angle : 0.672 14.258 13132 Z= 0.341 Chirality : 0.043 0.177 1466 Planarity : 0.005 0.060 1685 Dihedral : 15.640 88.304 3648 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % 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: -0.64 (0.23), residues: 1165 helix: 0.16 (0.19), residues: 693 sheet: -1.96 (0.87), residues: 33 loop : -1.11 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.008 0.001 HIS C 355 PHE 0.025 0.001 PHE A 402 TYR 0.035 0.001 TYR A 570 ARG 0.004 0.000 ARG A 707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 1.231 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: C 224 GLN cc_start: 0.8751 (tt0) cc_final: 0.8315 (tt0) REVERT: C 315 ASP cc_start: 0.5268 (m-30) cc_final: 0.4996 (m-30) REVERT: C 342 PHE cc_start: 0.8383 (m-80) cc_final: 0.8137 (m-10) REVERT: C 351 ASN cc_start: 0.8171 (p0) cc_final: 0.7504 (t0) REVERT: A 341 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 411 MET cc_start: 0.7919 (mtp) cc_final: 0.7653 (mtm) REVERT: A 566 PHE cc_start: 0.8645 (t80) cc_final: 0.8074 (t80) REVERT: A 632 LYS cc_start: 0.9272 (ptpt) cc_final: 0.9037 (ptpt) REVERT: A 640 LEU cc_start: 0.9081 (mp) cc_final: 0.8841 (pp) REVERT: A 664 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8663 (mppt) REVERT: A 701 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8869 (tptt) REVERT: B 31 LEU cc_start: 0.8989 (mm) cc_final: 0.8459 (tp) REVERT: B 60 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8131 (tm-30) REVERT: R 25 LYS cc_start: 0.8187 (pttm) cc_final: 0.7875 (pttm) REVERT: D 57 SER cc_start: 0.6427 (t) cc_final: 0.6051 (m) REVERT: D 69 TYR cc_start: 0.8907 (t80) cc_final: 0.8566 (t80) REVERT: D 105 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8156 (ttp-170) REVERT: D 115 TRP cc_start: 0.8396 (p-90) cc_final: 0.8153 (p-90) outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.2478 time to fit residues: 81.2810 Evaluate side-chains 161 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.0040 chunk 87 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9716 Z= 0.190 Angle : 0.634 11.544 13132 Z= 0.324 Chirality : 0.042 0.154 1466 Planarity : 0.004 0.059 1685 Dihedral : 4.146 21.913 1267 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.61 % Allowed : 10.07 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1165 helix: 0.89 (0.19), residues: 700 sheet: -2.02 (0.82), residues: 33 loop : -1.21 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 303 HIS 0.010 0.001 HIS A 524 PHE 0.024 0.002 PHE A 402 TYR 0.029 0.002 TYR A 570 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 ASP cc_start: 0.5317 (m-30) cc_final: 0.5058 (m-30) REVERT: C 351 ASN cc_start: 0.7864 (p0) cc_final: 0.7584 (t0) REVERT: C 376 TRP cc_start: 0.5171 (t-100) cc_final: 0.4703 (t-100) REVERT: A 43 MET cc_start: 0.8984 (tpp) cc_final: 0.8754 (tpp) REVERT: A 199 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8346 (tpp-160) REVERT: A 409 THR cc_start: 0.8638 (p) cc_final: 0.8351 (t) REVERT: A 566 PHE cc_start: 0.8599 (t80) cc_final: 0.8204 (t80) REVERT: A 632 LYS cc_start: 0.9372 (ptpt) cc_final: 0.9148 (ptpp) REVERT: A 664 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8680 (mppt) REVERT: A 701 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8873 (tptt) REVERT: A 719 MET cc_start: 0.4332 (tpp) cc_final: 0.4076 (tpp) REVERT: B 14 PHE cc_start: 0.7820 (m-80) cc_final: 0.7567 (m-80) REVERT: B 60 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 157 ASN cc_start: 0.8650 (p0) cc_final: 0.8385 (p0) REVERT: R 25 LYS cc_start: 0.8068 (pttm) cc_final: 0.7803 (pttm) REVERT: D 57 SER cc_start: 0.6573 (t) cc_final: 0.6218 (p) REVERT: D 61 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7806 (mmm-85) REVERT: D 133 ASP cc_start: 0.7711 (p0) cc_final: 0.7100 (t0) outliers start: 17 outliers final: 8 residues processed: 193 average time/residue: 0.2221 time to fit residues: 59.7281 Evaluate side-chains 155 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9716 Z= 0.217 Angle : 0.606 11.120 13132 Z= 0.313 Chirality : 0.041 0.179 1466 Planarity : 0.004 0.057 1685 Dihedral : 4.021 22.287 1267 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.62 % 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: 0.20 (0.24), residues: 1165 helix: 1.03 (0.19), residues: 699 sheet: -2.38 (0.87), residues: 28 loop : -1.13 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 303 HIS 0.019 0.001 HIS C 309 PHE 0.024 0.002 PHE C 342 TYR 0.026 0.002 TYR A 377 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 ASP cc_start: 0.5304 (m-30) cc_final: 0.5048 (m-30) REVERT: C 351 ASN cc_start: 0.7970 (p0) cc_final: 0.7720 (t0) REVERT: A 261 MET cc_start: 0.8840 (mtp) cc_final: 0.8392 (ttt) REVERT: A 409 THR cc_start: 0.8628 (p) cc_final: 0.8290 (t) REVERT: A 566 PHE cc_start: 0.8553 (t80) cc_final: 0.8315 (t80) REVERT: A 632 LYS cc_start: 0.9382 (ptpt) cc_final: 0.9132 (ptpp) REVERT: A 640 LEU cc_start: 0.9168 (mt) cc_final: 0.8558 (pp) REVERT: A 664 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8705 (mppt) REVERT: A 701 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8887 (tptt) REVERT: B 60 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 157 ASN cc_start: 0.8636 (p0) cc_final: 0.8405 (p0) REVERT: D 57 SER cc_start: 0.6720 (t) cc_final: 0.6357 (m) REVERT: D 61 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7883 (mmm-85) REVERT: D 115 TRP cc_start: 0.8324 (p-90) cc_final: 0.7915 (p-90) REVERT: D 133 ASP cc_start: 0.7649 (p0) cc_final: 0.6949 (t0) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2070 time to fit residues: 50.9401 Evaluate side-chains 161 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9716 Z= 0.201 Angle : 0.610 10.832 13132 Z= 0.312 Chirality : 0.040 0.224 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.981 21.389 1267 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.66 % Allowed : 14.62 % Favored : 82.72 % 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: 0.36 (0.24), residues: 1165 helix: 1.18 (0.19), residues: 694 sheet: -2.03 (0.78), residues: 33 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 303 HIS 0.012 0.001 HIS C 309 PHE 0.023 0.002 PHE C 342 TYR 0.033 0.002 TYR A 570 ARG 0.003 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 PHE cc_start: 0.2702 (OUTLIER) cc_final: 0.2243 (m-80) REVERT: C 315 ASP cc_start: 0.5282 (m-30) cc_final: 0.5015 (m-30) REVERT: C 351 ASN cc_start: 0.7973 (p0) cc_final: 0.7765 (t0) REVERT: A 199 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8336 (tpp-160) REVERT: A 261 MET cc_start: 0.8812 (mtp) cc_final: 0.8585 (ttm) REVERT: A 409 THR cc_start: 0.8628 (p) cc_final: 0.8292 (t) REVERT: A 640 LEU cc_start: 0.9177 (mt) cc_final: 0.8693 (pp) REVERT: A 664 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8702 (mppt) REVERT: A 701 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8891 (tptt) REVERT: B 60 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 157 ASN cc_start: 0.8638 (p0) cc_final: 0.8405 (p0) REVERT: D 57 SER cc_start: 0.6523 (t) cc_final: 0.6296 (m) REVERT: D 61 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7886 (mmm-85) REVERT: D 115 TRP cc_start: 0.8283 (p-90) cc_final: 0.7909 (p-90) REVERT: D 133 ASP cc_start: 0.7598 (p0) cc_final: 0.6929 (t0) outliers start: 28 outliers final: 21 residues processed: 174 average time/residue: 0.2097 time to fit residues: 52.8922 Evaluate side-chains 168 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9716 Z= 0.234 Angle : 0.618 9.984 13132 Z= 0.316 Chirality : 0.041 0.170 1466 Planarity : 0.004 0.057 1685 Dihedral : 3.973 22.638 1267 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.75 % Allowed : 17.19 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1165 helix: 1.20 (0.19), residues: 695 sheet: -2.07 (0.77), residues: 33 loop : -1.02 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 303 HIS 0.011 0.001 HIS C 309 PHE 0.021 0.002 PHE C 342 TYR 0.025 0.002 TYR A 278 ARG 0.005 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.2156 (m-80) REVERT: C 315 ASP cc_start: 0.5254 (m-30) cc_final: 0.4920 (m-30) REVERT: C 351 ASN cc_start: 0.8028 (p0) cc_final: 0.7701 (t0) REVERT: A 37 MET cc_start: 0.9052 (ppp) cc_final: 0.8818 (ppp) REVERT: A 199 ARG cc_start: 0.8543 (tpp-160) cc_final: 0.8297 (tpp-160) REVERT: A 261 MET cc_start: 0.8824 (mtp) cc_final: 0.8404 (ttt) REVERT: A 305 THR cc_start: 0.9207 (m) cc_final: 0.8739 (p) REVERT: A 409 THR cc_start: 0.8645 (p) cc_final: 0.8317 (t) REVERT: A 570 TYR cc_start: 0.7479 (p90) cc_final: 0.7148 (p90) REVERT: A 633 MET cc_start: 0.8899 (tpt) cc_final: 0.8063 (pmm) REVERT: A 640 LEU cc_start: 0.9185 (mt) cc_final: 0.8739 (pp) REVERT: A 664 LYS cc_start: 0.9225 (mmtm) cc_final: 0.8694 (mppt) REVERT: A 701 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8901 (tptt) REVERT: B 60 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 126 MET cc_start: 0.8373 (tmm) cc_final: 0.7937 (mtt) REVERT: B 157 ASN cc_start: 0.8669 (p0) cc_final: 0.8415 (p0) REVERT: D 57 SER cc_start: 0.6519 (t) cc_final: 0.6315 (m) REVERT: D 61 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7916 (mmm-85) REVERT: D 115 TRP cc_start: 0.8320 (p-90) cc_final: 0.7826 (p-90) REVERT: D 133 ASP cc_start: 0.7631 (p0) cc_final: 0.6931 (t0) outliers start: 29 outliers final: 21 residues processed: 166 average time/residue: 0.2150 time to fit residues: 51.5389 Evaluate side-chains 160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9716 Z= 0.196 Angle : 0.614 9.475 13132 Z= 0.314 Chirality : 0.041 0.176 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.983 21.752 1267 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.94 % Allowed : 18.14 % Favored : 78.92 % 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: 0.47 (0.24), residues: 1165 helix: 1.27 (0.20), residues: 695 sheet: -2.13 (0.79), residues: 33 loop : -1.02 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 303 HIS 0.012 0.001 HIS A 524 PHE 0.024 0.002 PHE A 498 TYR 0.021 0.002 TYR A 278 ARG 0.006 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6200 (p90) cc_final: 0.5800 (p90) REVERT: C 289 PHE cc_start: 0.2527 (OUTLIER) cc_final: 0.1954 (m-80) REVERT: C 315 ASP cc_start: 0.5201 (m-30) cc_final: 0.4903 (m-30) REVERT: C 351 ASN cc_start: 0.7923 (p0) cc_final: 0.7619 (t0) REVERT: A 37 MET cc_start: 0.9025 (ppp) cc_final: 0.8809 (ppp) REVERT: A 199 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.8281 (tpp-160) REVERT: A 409 THR cc_start: 0.8622 (p) cc_final: 0.8294 (t) REVERT: A 570 TYR cc_start: 0.7525 (p90) cc_final: 0.7082 (p90) REVERT: A 640 LEU cc_start: 0.9175 (mt) cc_final: 0.8763 (pp) REVERT: A 664 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8689 (mppt) REVERT: A 701 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8860 (tptt) REVERT: B 60 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 157 ASN cc_start: 0.8659 (p0) cc_final: 0.8400 (p0) REVERT: D 61 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7887 (mmm-85) REVERT: D 115 TRP cc_start: 0.8279 (p-90) cc_final: 0.7967 (p-90) REVERT: D 133 ASP cc_start: 0.7649 (p0) cc_final: 0.6968 (t0) REVERT: D 145 MET cc_start: 0.7871 (tmm) cc_final: 0.7627 (tmm) REVERT: D 147 CYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6873 (p) outliers start: 31 outliers final: 22 residues processed: 166 average time/residue: 0.2002 time to fit residues: 48.0018 Evaluate side-chains 159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 343 HIS ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9716 Z= 0.234 Angle : 0.643 12.058 13132 Z= 0.330 Chirality : 0.042 0.174 1466 Planarity : 0.004 0.058 1685 Dihedral : 4.024 21.572 1267 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.23 % Allowed : 19.18 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1165 helix: 1.21 (0.20), residues: 692 sheet: -2.23 (0.75), residues: 33 loop : -1.04 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 303 HIS 0.012 0.001 HIS A 524 PHE 0.017 0.002 PHE C 342 TYR 0.020 0.002 TYR A 278 ARG 0.007 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6249 (p90) cc_final: 0.5731 (p90) REVERT: C 289 PHE cc_start: 0.2513 (OUTLIER) cc_final: 0.2100 (m-80) REVERT: C 315 ASP cc_start: 0.5253 (m-30) cc_final: 0.4943 (m-30) REVERT: C 351 ASN cc_start: 0.7994 (p0) cc_final: 0.7770 (t0) REVERT: A 37 MET cc_start: 0.9014 (ppp) cc_final: 0.8791 (ppp) REVERT: A 199 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8277 (tpp-160) REVERT: A 409 THR cc_start: 0.8647 (p) cc_final: 0.8308 (t) REVERT: A 570 TYR cc_start: 0.7669 (p90) cc_final: 0.7123 (p90) REVERT: A 633 MET cc_start: 0.8916 (tpt) cc_final: 0.8084 (pmm) REVERT: A 640 LEU cc_start: 0.9177 (mt) cc_final: 0.8784 (pp) REVERT: A 664 LYS cc_start: 0.9240 (mmtm) cc_final: 0.8699 (mppt) REVERT: A 701 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8854 (tptt) REVERT: B 60 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 126 MET cc_start: 0.8434 (tmm) cc_final: 0.7995 (mtt) REVERT: B 157 ASN cc_start: 0.8671 (p0) cc_final: 0.8407 (p0) REVERT: D 61 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7857 (mmm-85) REVERT: D 115 TRP cc_start: 0.8287 (p-90) cc_final: 0.7979 (p-90) REVERT: D 133 ASP cc_start: 0.7640 (p0) cc_final: 0.6942 (t0) REVERT: D 147 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6835 (p) outliers start: 34 outliers final: 25 residues processed: 161 average time/residue: 0.2021 time to fit residues: 47.2778 Evaluate side-chains 159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS A 35 GLN A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9716 Z= 0.191 Angle : 0.641 10.578 13132 Z= 0.322 Chirality : 0.041 0.167 1466 Planarity : 0.004 0.058 1685 Dihedral : 4.012 22.680 1267 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.51 % Allowed : 18.90 % Favored : 77.59 % 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: 0.39 (0.24), residues: 1165 helix: 1.21 (0.19), residues: 690 sheet: -2.31 (0.72), residues: 33 loop : -1.02 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 303 HIS 0.012 0.001 HIS A 524 PHE 0.021 0.001 PHE C 370 TYR 0.022 0.002 TYR A 570 ARG 0.006 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6129 (p90) cc_final: 0.5601 (p90) REVERT: C 289 PHE cc_start: 0.2508 (OUTLIER) cc_final: 0.1980 (m-80) REVERT: C 315 ASP cc_start: 0.5179 (m-30) cc_final: 0.4862 (m-30) REVERT: C 351 ASN cc_start: 0.7987 (p0) cc_final: 0.7736 (t0) REVERT: A 52 TYR cc_start: 0.8905 (t80) cc_final: 0.8675 (t80) REVERT: A 319 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 508 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A 570 TYR cc_start: 0.7711 (p90) cc_final: 0.7125 (p90) REVERT: A 633 MET cc_start: 0.8895 (tpt) cc_final: 0.8058 (pmm) REVERT: A 640 LEU cc_start: 0.9177 (mt) cc_final: 0.8789 (pp) REVERT: A 664 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8700 (mppt) REVERT: A 701 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8846 (tptt) REVERT: B 60 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 126 MET cc_start: 0.8364 (tmm) cc_final: 0.8099 (mtt) REVERT: B 157 ASN cc_start: 0.8666 (p0) cc_final: 0.8325 (p0) REVERT: D 61 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7866 (mmm-85) REVERT: D 115 TRP cc_start: 0.8283 (p-90) cc_final: 0.7969 (p-90) REVERT: D 133 ASP cc_start: 0.7649 (p0) cc_final: 0.6937 (t0) REVERT: D 140 MET cc_start: 0.7989 (mtt) cc_final: 0.7695 (mtm) REVERT: D 145 MET cc_start: 0.7748 (tmm) cc_final: 0.7489 (tmm) REVERT: D 147 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6826 (p) outliers start: 37 outliers final: 23 residues processed: 179 average time/residue: 0.2155 time to fit residues: 55.4378 Evaluate side-chains 160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0060 chunk 106 optimal weight: 0.0270 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9716 Z= 0.188 Angle : 0.676 12.238 13132 Z= 0.340 Chirality : 0.043 0.271 1466 Planarity : 0.004 0.067 1685 Dihedral : 4.036 22.377 1267 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.56 % Allowed : 20.32 % Favored : 77.11 % 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: 0.38 (0.24), residues: 1165 helix: 1.20 (0.19), residues: 691 sheet: -2.36 (0.71), residues: 33 loop : -1.04 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 303 HIS 0.014 0.001 HIS A 524 PHE 0.014 0.001 PHE B 145 TYR 0.034 0.001 TYR A 278 ARG 0.005 0.000 ARG A 745 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6030 (p90) cc_final: 0.5524 (p90) REVERT: C 289 PHE cc_start: 0.2479 (OUTLIER) cc_final: 0.1968 (m-80) REVERT: C 315 ASP cc_start: 0.5240 (m-30) cc_final: 0.4983 (m-30) REVERT: C 351 ASN cc_start: 0.7946 (p0) cc_final: 0.7637 (t0) REVERT: A 52 TYR cc_start: 0.8845 (t80) cc_final: 0.8609 (t80) REVERT: A 319 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 450 MET cc_start: 0.8838 (tpp) cc_final: 0.8551 (tpp) REVERT: A 508 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: A 570 TYR cc_start: 0.7768 (p90) cc_final: 0.7205 (p90) REVERT: A 633 MET cc_start: 0.8895 (tpt) cc_final: 0.8067 (pmm) REVERT: A 640 LEU cc_start: 0.9180 (mt) cc_final: 0.8814 (pp) REVERT: A 664 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8705 (mppt) REVERT: A 701 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8839 (tptt) REVERT: B 60 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 126 MET cc_start: 0.8332 (tmm) cc_final: 0.8050 (mtt) REVERT: D 61 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7840 (mmm-85) REVERT: D 115 TRP cc_start: 0.8263 (p-90) cc_final: 0.7945 (p-90) REVERT: D 133 ASP cc_start: 0.7647 (p0) cc_final: 0.6947 (t0) REVERT: D 140 MET cc_start: 0.7898 (mtt) cc_final: 0.7612 (mtm) REVERT: D 145 MET cc_start: 0.7697 (tmm) cc_final: 0.7410 (tmm) REVERT: D 147 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6958 (p) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.1980 time to fit residues: 45.7721 Evaluate side-chains 154 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9716 Z= 0.232 Angle : 0.679 8.917 13132 Z= 0.342 Chirality : 0.043 0.201 1466 Planarity : 0.004 0.069 1685 Dihedral : 4.050 22.560 1267 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.47 % Allowed : 20.89 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1165 helix: 1.15 (0.19), residues: 700 sheet: -2.71 (0.78), residues: 27 loop : -0.93 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 303 HIS 0.013 0.001 HIS A 524 PHE 0.019 0.001 PHE A 391 TYR 0.031 0.002 TYR A 278 ARG 0.007 0.000 ARG A 745 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6087 (p90) cc_final: 0.5579 (p90) REVERT: C 289 PHE cc_start: 0.2477 (OUTLIER) cc_final: 0.1994 (m-80) REVERT: C 315 ASP cc_start: 0.5273 (m-30) cc_final: 0.5004 (m-30) REVERT: C 351 ASN cc_start: 0.8062 (p0) cc_final: 0.7664 (t0) REVERT: A 52 TYR cc_start: 0.8900 (t80) cc_final: 0.8662 (t80) REVERT: A 319 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 331 ASP cc_start: 0.8075 (t0) cc_final: 0.7736 (t0) REVERT: A 450 MET cc_start: 0.8846 (tpp) cc_final: 0.8548 (tpp) REVERT: A 508 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: A 570 TYR cc_start: 0.7832 (p90) cc_final: 0.7289 (p90) REVERT: A 633 MET cc_start: 0.8914 (tpt) cc_final: 0.8076 (pmm) REVERT: A 640 LEU cc_start: 0.9188 (mt) cc_final: 0.8828 (pp) REVERT: A 664 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8716 (mppt) REVERT: A 701 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8857 (tptt) REVERT: B 60 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 126 MET cc_start: 0.8329 (tmm) cc_final: 0.8093 (mtt) REVERT: R 25 LYS cc_start: 0.8419 (pttm) cc_final: 0.8139 (pttm) REVERT: D 61 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7864 (mmm-85) REVERT: D 133 ASP cc_start: 0.7671 (p0) cc_final: 0.6956 (t0) REVERT: D 140 MET cc_start: 0.7899 (mtt) cc_final: 0.7611 (mtm) REVERT: D 145 MET cc_start: 0.7777 (tmm) cc_final: 0.7506 (tmm) REVERT: D 147 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6992 (p) outliers start: 26 outliers final: 18 residues processed: 158 average time/residue: 0.2101 time to fit residues: 48.2723 Evaluate side-chains 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 38 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.123919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087851 restraints weight = 24417.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086053 restraints weight = 15289.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086714 restraints weight = 13744.912| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 9716 Z= 0.327 Angle : 0.996 59.184 13132 Z= 0.548 Chirality : 0.043 0.365 1466 Planarity : 0.004 0.069 1685 Dihedral : 4.041 22.481 1267 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.56 % Allowed : 20.70 % Favored : 76.73 % Cbeta Deviations : 0.09 % 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: 0.41 (0.24), residues: 1165 helix: 1.16 (0.19), residues: 700 sheet: -2.71 (0.78), residues: 27 loop : -0.93 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 303 HIS 0.011 0.001 HIS A 524 PHE 0.017 0.002 PHE A 391 TYR 0.029 0.002 TYR A 278 ARG 0.005 0.000 ARG A 745 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.82 seconds wall clock time: 44 minutes 30.93 seconds (2670.93 seconds total)