Starting phenix.real_space_refine on Thu Jan 16 13:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_61550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_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/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_61550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_61550.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_61550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkb_61550/01_2025/9jkb_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.07, per 1000 atoms: 0.64 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 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: 0.89 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: 2.93 Time building geometry restraints manager: 2.99 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: 21.030 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.350 ------------------------------------------------------------------------------- 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 : 1.099 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: 0.2667 time to fit residues: 87.1644 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 : 1.249 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.129562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095277 restraints weight = 26312.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095027 restraints weight = 14448.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095728 restraints weight = 12094.128| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 ASP cc_start: 0.5394 (m-30) cc_final: 0.5084 (m-30) REVERT: C 370 PHE cc_start: 0.7505 (m-10) cc_final: 0.7224 (m-10) REVERT: C 376 TRP cc_start: 0.6230 (t-100) cc_final: 0.5772 (t-100) REVERT: A 43 MET cc_start: 0.8964 (tpp) cc_final: 0.8743 (tpp) REVERT: A 199 ARG cc_start: 0.8455 (tpp-160) cc_final: 0.8205 (tpp-160) REVERT: A 409 THR cc_start: 0.8629 (p) cc_final: 0.8337 (t) REVERT: A 566 PHE cc_start: 0.8503 (t80) cc_final: 0.8123 (t80) REVERT: A 632 LYS cc_start: 0.9346 (ptpt) cc_final: 0.9128 (ptpp) REVERT: A 664 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8683 (mppt) REVERT: A 701 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8868 (tptt) REVERT: A 719 MET cc_start: 0.4292 (tpp) cc_final: 0.4043 (tpp) REVERT: B 14 PHE cc_start: 0.7753 (m-80) cc_final: 0.7519 (m-80) REVERT: B 60 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 157 ASN cc_start: 0.8611 (p0) cc_final: 0.8353 (p0) REVERT: R 25 LYS cc_start: 0.8014 (pttm) cc_final: 0.7767 (pttm) REVERT: D 57 SER cc_start: 0.6540 (t) cc_final: 0.6206 (p) REVERT: D 61 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7710 (mmm-85) REVERT: D 133 ASP cc_start: 0.7445 (p0) cc_final: 0.6893 (t0) outliers start: 17 outliers final: 8 residues processed: 193 average time/residue: 0.2277 time to fit residues: 61.2150 Evaluate side-chains 154 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 89 optimal weight: 0.0470 chunk 82 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 C 351 ASN A 253 GLN ** A 404 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.132370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096724 restraints weight = 25200.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096134 restraints weight = 14275.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096347 restraints weight = 11621.068| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9716 Z= 0.189 Angle : 0.605 11.714 13132 Z= 0.310 Chirality : 0.041 0.185 1466 Planarity : 0.004 0.057 1685 Dihedral : 4.004 22.095 1267 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.99 % Allowed : 13.01 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1165 helix: 1.06 (0.19), residues: 699 sheet: -2.32 (0.87), residues: 28 loop : -1.14 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 303 HIS 0.018 0.001 HIS C 309 PHE 0.024 0.002 PHE C 342 TYR 0.024 0.002 TYR A 278 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 179 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 ASP cc_start: 0.5376 (m-30) cc_final: 0.5073 (m-30) REVERT: C 351 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7814 (p0) REVERT: A 199 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8145 (tpp-160) REVERT: A 261 MET cc_start: 0.8738 (mtp) cc_final: 0.8322 (ttt) REVERT: A 409 THR cc_start: 0.8617 (p) cc_final: 0.8352 (t) REVERT: A 632 LYS cc_start: 0.9323 (ptpt) cc_final: 0.9095 (ptpp) REVERT: A 640 LEU cc_start: 0.9160 (mt) cc_final: 0.8606 (pp) REVERT: A 664 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8702 (mppt) REVERT: A 701 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8863 (tptt) REVERT: A 719 MET cc_start: 0.4503 (tpp) cc_final: 0.4267 (tpp) REVERT: B 60 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 82 THR cc_start: 0.7675 (p) cc_final: 0.7472 (t) REVERT: B 157 ASN cc_start: 0.8564 (p0) cc_final: 0.8336 (p0) REVERT: D 57 SER cc_start: 0.6732 (t) cc_final: 0.6409 (m) REVERT: D 61 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7829 (mmm-85) REVERT: D 115 TRP cc_start: 0.8536 (p-90) cc_final: 0.8086 (p-90) REVERT: D 133 ASP cc_start: 0.7552 (p0) cc_final: 0.6869 (t0) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.2087 time to fit residues: 50.6310 Evaluate side-chains 159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 351 ASN 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 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 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 60 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 351 ASN A 253 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.130466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094782 restraints weight = 24979.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094553 restraints weight = 12783.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095557 restraints weight = 10035.730| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9716 Z= 0.194 Angle : 0.603 11.018 13132 Z= 0.310 Chirality : 0.041 0.263 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.980 21.164 1267 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.75 % Allowed : 14.81 % Favored : 82.43 % 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: 0.35 (0.24), residues: 1165 helix: 1.18 (0.19), residues: 694 sheet: -1.98 (0.78), residues: 33 loop : -1.11 (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 A 498 TYR 0.029 0.002 TYR A 570 ARG 0.004 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 181 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 PHE cc_start: 0.2874 (OUTLIER) cc_final: 0.2418 (m-80) REVERT: C 315 ASP cc_start: 0.5385 (m-30) cc_final: 0.4984 (m-30) REVERT: A 199 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.8186 (tpp-160) REVERT: A 261 MET cc_start: 0.8709 (mtp) cc_final: 0.8447 (ttm) REVERT: A 409 THR cc_start: 0.8585 (p) cc_final: 0.8247 (t) REVERT: A 570 TYR cc_start: 0.7350 (p90) cc_final: 0.7016 (p90) REVERT: A 640 LEU cc_start: 0.9191 (mt) cc_final: 0.8726 (pp) REVERT: A 664 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8687 (mppt) REVERT: A 701 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8871 (tptt) REVERT: B 60 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 157 ASN cc_start: 0.8596 (p0) cc_final: 0.8364 (p0) REVERT: D 57 SER cc_start: 0.6528 (t) cc_final: 0.6320 (m) REVERT: D 61 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7791 (mmm-85) REVERT: D 115 TRP cc_start: 0.8560 (p-90) cc_final: 0.8118 (p-90) REVERT: D 133 ASP cc_start: 0.7424 (p0) cc_final: 0.6790 (t0) outliers start: 29 outliers final: 22 residues processed: 168 average time/residue: 0.2147 time to fit residues: 51.5719 Evaluate side-chains 160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 C residue 351 ASN 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 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 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 46 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 351 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.129419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094700 restraints weight = 26096.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093670 restraints weight = 14927.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.094598 restraints weight = 12362.751| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9716 Z= 0.234 Angle : 0.606 10.078 13132 Z= 0.312 Chirality : 0.041 0.174 1466 Planarity : 0.004 0.057 1685 Dihedral : 3.941 22.530 1267 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.13 % Allowed : 16.14 % Favored : 80.72 % 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: 0.46 (0.24), residues: 1165 helix: 1.27 (0.19), residues: 694 sheet: -2.00 (0.78), residues: 33 loop : -1.05 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 303 HIS 0.011 0.001 HIS C 309 PHE 0.025 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 184 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 PHE cc_start: 0.2985 (OUTLIER) cc_final: 0.2443 (m-80) REVERT: C 315 ASP cc_start: 0.5408 (m-30) cc_final: 0.5022 (m-30) REVERT: A 37 MET cc_start: 0.9019 (ppp) cc_final: 0.8800 (ppp) REVERT: A 199 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8145 (tpp-160) REVERT: A 305 THR cc_start: 0.9184 (m) cc_final: 0.8752 (p) REVERT: A 409 THR cc_start: 0.8604 (p) cc_final: 0.8276 (t) REVERT: A 570 TYR cc_start: 0.7415 (p90) cc_final: 0.6991 (p90) REVERT: A 633 MET cc_start: 0.8889 (tpt) cc_final: 0.8085 (pmm) REVERT: A 640 LEU cc_start: 0.9212 (mt) cc_final: 0.8774 (pp) REVERT: A 664 LYS cc_start: 0.9237 (mmtm) cc_final: 0.8685 (mppt) REVERT: A 701 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8896 (tptt) REVERT: B 60 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 157 ASN cc_start: 0.8606 (p0) cc_final: 0.8360 (p0) REVERT: D 61 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7829 (mmm-85) REVERT: D 115 TRP cc_start: 0.8532 (p-90) cc_final: 0.8112 (p-90) REVERT: D 133 ASP cc_start: 0.7457 (p0) cc_final: 0.6820 (t0) REVERT: D 140 MET cc_start: 0.8069 (ptp) cc_final: 0.7554 (mtt) REVERT: D 145 MET cc_start: 0.7841 (tmm) cc_final: 0.7604 (tmm) outliers start: 33 outliers final: 22 residues processed: 170 average time/residue: 0.2201 time to fit residues: 54.6406 Evaluate side-chains 158 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 C residue 351 ASN 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 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 539 VAL Chi-restraints excluded: chain A residue 585 LEU 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 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 54 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 351 ASN A 253 GLN ** A 404 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.123874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088104 restraints weight = 23924.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086887 restraints weight = 13994.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087676 restraints weight = 12001.236| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9716 Z= 0.228 Angle : 0.619 10.535 13132 Z= 0.317 Chirality : 0.041 0.179 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.942 21.774 1267 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.75 % Allowed : 18.71 % Favored : 78.54 % 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: 0.51 (0.25), residues: 1165 helix: 1.32 (0.20), residues: 693 sheet: -2.04 (0.78), residues: 33 loop : -1.04 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 303 HIS 0.019 0.002 HIS C 309 PHE 0.023 0.002 PHE A 498 TYR 0.021 0.002 TYR A 278 ARG 0.005 0.000 ARG A 745 *********************** 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 179 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6555 (p90) cc_final: 0.6123 (p90) REVERT: C 289 PHE cc_start: 0.2965 (OUTLIER) cc_final: 0.2345 (m-80) REVERT: C 315 ASP cc_start: 0.5376 (m-30) cc_final: 0.5017 (m-30) REVERT: C 357 TRP cc_start: 0.7924 (p-90) cc_final: 0.7401 (p-90) REVERT: C 370 PHE cc_start: 0.7579 (m-10) cc_final: 0.7347 (m-10) REVERT: A 199 ARG cc_start: 0.8401 (tpp-160) cc_final: 0.8197 (tpp-160) REVERT: A 261 MET cc_start: 0.8351 (ttp) cc_final: 0.7596 (ttp) REVERT: A 322 MET cc_start: 0.9204 (tpt) cc_final: 0.8776 (tpt) REVERT: A 409 THR cc_start: 0.8611 (p) cc_final: 0.8284 (t) REVERT: A 570 TYR cc_start: 0.7487 (p90) cc_final: 0.6942 (p90) REVERT: A 640 LEU cc_start: 0.9197 (mt) cc_final: 0.8787 (pp) REVERT: A 664 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8699 (mppt) REVERT: A 701 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8845 (tptt) REVERT: B 60 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 126 MET cc_start: 0.8487 (tmm) cc_final: 0.8020 (mtt) REVERT: B 157 ASN cc_start: 0.8584 (p0) cc_final: 0.8338 (p0) REVERT: D 61 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7783 (mmm-85) REVERT: D 115 TRP cc_start: 0.8542 (p-90) cc_final: 0.7965 (p-90) REVERT: D 133 ASP cc_start: 0.7441 (p0) cc_final: 0.6802 (t0) REVERT: D 140 MET cc_start: 0.8127 (ptp) cc_final: 0.7615 (mtt) outliers start: 29 outliers final: 21 residues processed: 167 average time/residue: 0.2061 time to fit residues: 50.0982 Evaluate side-chains 163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 539 VAL Chi-restraints excluded: chain A residue 585 LEU 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 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 83 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 351 ASN A 35 GLN A 343 HIS ** A 404 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.122954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086691 restraints weight = 24484.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085201 restraints weight = 14516.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086323 restraints weight = 12531.403| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9716 Z= 0.235 Angle : 0.622 9.624 13132 Z= 0.320 Chirality : 0.041 0.170 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.978 21.537 1267 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.61 % Allowed : 18.80 % 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: 0.45 (0.24), residues: 1165 helix: 1.25 (0.19), residues: 697 sheet: -2.21 (0.75), residues: 33 loop : -1.02 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 303 HIS 0.013 0.001 HIS C 309 PHE 0.016 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 183 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6476 (p90) cc_final: 0.5996 (p90) REVERT: C 289 PHE cc_start: 0.3030 (OUTLIER) cc_final: 0.2505 (m-80) REVERT: C 315 ASP cc_start: 0.5351 (m-30) cc_final: 0.5002 (m-30) REVERT: C 357 TRP cc_start: 0.7850 (p-90) cc_final: 0.7515 (p-90) REVERT: C 370 PHE cc_start: 0.7707 (m-10) cc_final: 0.7445 (m-10) REVERT: A 199 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.8160 (tpp-160) REVERT: A 253 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 261 MET cc_start: 0.8267 (ttp) cc_final: 0.7534 (ttp) REVERT: A 322 MET cc_start: 0.9191 (tpt) cc_final: 0.8723 (tpt) REVERT: A 508 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: A 570 TYR cc_start: 0.7594 (p90) cc_final: 0.7082 (p90) REVERT: A 633 MET cc_start: 0.8790 (tpt) cc_final: 0.8026 (pmm) REVERT: A 640 LEU cc_start: 0.9188 (mt) cc_final: 0.8797 (pp) REVERT: A 664 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8713 (mppt) REVERT: A 701 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8843 (tptt) REVERT: B 60 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 126 MET cc_start: 0.8461 (tmm) cc_final: 0.8137 (mtt) REVERT: B 157 ASN cc_start: 0.8573 (p0) cc_final: 0.8325 (p0) REVERT: D 61 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7713 (mmm-85) REVERT: D 115 TRP cc_start: 0.8558 (p-90) cc_final: 0.7975 (p-90) REVERT: D 133 ASP cc_start: 0.7425 (p0) cc_final: 0.6751 (t0) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 0.2143 time to fit residues: 51.9285 Evaluate side-chains 159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 211 LEU 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 508 PHE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 672 TYR 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 104 ILE 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 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 87 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 chunk 61 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088537 restraints weight = 24732.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087204 restraints weight = 15511.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087756 restraints weight = 13306.724| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9716 Z= 0.190 Angle : 0.634 9.322 13132 Z= 0.318 Chirality : 0.041 0.153 1466 Planarity : 0.004 0.058 1685 Dihedral : 3.984 22.868 1267 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.85 % Allowed : 20.51 % 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: 0.44 (0.24), residues: 1165 helix: 1.22 (0.20), residues: 698 sheet: -2.25 (0.73), residues: 33 loop : -1.00 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 303 HIS 0.015 0.002 HIS A 524 PHE 0.014 0.001 PHE C 342 TYR 0.021 0.001 TYR A 570 ARG 0.007 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 182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6367 (p90) cc_final: 0.5873 (p90) REVERT: C 289 PHE cc_start: 0.3054 (OUTLIER) cc_final: 0.2447 (m-80) REVERT: C 315 ASP cc_start: 0.5500 (m-30) cc_final: 0.5174 (m-30) REVERT: C 370 PHE cc_start: 0.7701 (m-10) cc_final: 0.7391 (m-10) REVERT: A 52 TYR cc_start: 0.8833 (t80) cc_final: 0.8617 (t80) REVERT: A 253 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: A 261 MET cc_start: 0.8185 (ttp) cc_final: 0.7523 (ttp) REVERT: A 322 MET cc_start: 0.9181 (tpt) cc_final: 0.8724 (tpt) REVERT: A 331 ASP cc_start: 0.7866 (t0) cc_final: 0.7533 (t0) REVERT: A 450 MET cc_start: 0.8702 (tpp) cc_final: 0.8415 (tpp) REVERT: A 508 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: A 570 TYR cc_start: 0.7547 (p90) cc_final: 0.7161 (p90) REVERT: A 633 MET cc_start: 0.8782 (tpt) cc_final: 0.8008 (pmm) REVERT: A 640 LEU cc_start: 0.9177 (mt) cc_final: 0.8811 (pp) REVERT: A 664 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8708 (mppt) REVERT: A 701 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8832 (tptt) REVERT: B 60 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 157 ASN cc_start: 0.8560 (p0) cc_final: 0.8255 (p0) REVERT: D 61 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7772 (mmm-85) REVERT: D 115 TRP cc_start: 0.8536 (p-90) cc_final: 0.7980 (p-90) REVERT: D 133 ASP cc_start: 0.7446 (p0) cc_final: 0.6771 (t0) REVERT: D 145 MET cc_start: 0.7879 (tmm) cc_final: 0.7369 (tmm) outliers start: 30 outliers final: 21 residues processed: 174 average time/residue: 0.2104 time to fit residues: 52.2495 Evaluate side-chains 156 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 508 PHE Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 585 LEU 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 127 ILE 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 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 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 113 optimal weight: 0.0070 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 81 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 106 optimal weight: 0.0060 chunk 36 optimal weight: 0.6980 overall best weight: 0.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 158 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.125415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095949 restraints weight = 24604.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093904 restraints weight = 27296.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094823 restraints weight = 25856.653| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3388 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= 0.179 Angle : 0.663 9.474 13132 Z= 0.333 Chirality : 0.042 0.238 1466 Planarity : 0.004 0.058 1685 Dihedral : 4.047 22.033 1267 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.18 % Allowed : 21.65 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1165 helix: 1.15 (0.19), residues: 707 sheet: -3.13 (0.77), residues: 25 loop : -0.96 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 303 HIS 0.013 0.001 HIS A 524 PHE 0.014 0.001 PHE A 742 TYR 0.033 0.001 TYR A 278 ARG 0.006 0.000 ARG B 81 *********************** 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 164 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.5884 (p90) cc_final: 0.5506 (p90) REVERT: C 289 PHE cc_start: 0.2533 (OUTLIER) cc_final: 0.2062 (m-80) REVERT: C 315 ASP cc_start: 0.5376 (m-30) cc_final: 0.5156 (m-30) REVERT: A 52 TYR cc_start: 0.8743 (t80) cc_final: 0.8531 (t80) REVERT: A 261 MET cc_start: 0.8154 (ttp) cc_final: 0.7506 (ttp) REVERT: A 322 MET cc_start: 0.9114 (tpt) cc_final: 0.8630 (tpt) REVERT: A 450 MET cc_start: 0.8704 (tpp) cc_final: 0.8471 (tpp) REVERT: A 570 TYR cc_start: 0.7108 (p90) cc_final: 0.6854 (p90) REVERT: A 633 MET cc_start: 0.8398 (tpt) cc_final: 0.7842 (pmm) REVERT: A 640 LEU cc_start: 0.9054 (mt) cc_final: 0.8775 (pp) REVERT: A 664 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8645 (mppt) REVERT: B 60 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 126 MET cc_start: 0.8160 (tmm) cc_final: 0.7687 (mtm) REVERT: D 61 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7744 (mmm-85) REVERT: D 115 TRP cc_start: 0.8089 (p-90) cc_final: 0.7770 (p-90) REVERT: D 133 ASP cc_start: 0.7137 (p0) cc_final: 0.6620 (t0) REVERT: D 140 MET cc_start: 0.8013 (mtm) cc_final: 0.7752 (mtt) REVERT: D 145 MET cc_start: 0.7772 (tmm) cc_final: 0.7220 (tmm) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.2119 time to fit residues: 48.8685 Evaluate side-chains 143 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 253 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 91 GLU 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 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089366 restraints weight = 24895.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087691 restraints weight = 15403.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088342 restraints weight = 13660.203| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9716 Z= 0.203 Angle : 0.669 9.212 13132 Z= 0.337 Chirality : 0.043 0.230 1466 Planarity : 0.004 0.058 1685 Dihedral : 4.017 21.986 1267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.09 % Allowed : 22.51 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1165 helix: 1.18 (0.19), residues: 706 sheet: -2.88 (0.78), residues: 27 loop : -0.97 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 303 HIS 0.013 0.001 HIS A 524 PHE 0.027 0.002 PHE A 498 TYR 0.030 0.002 TYR A 278 ARG 0.004 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 157 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 PHE cc_start: 0.6376 (p90) cc_final: 0.5907 (p90) REVERT: C 289 PHE cc_start: 0.2875 (OUTLIER) cc_final: 0.2375 (m-80) REVERT: C 315 ASP cc_start: 0.5399 (m-30) cc_final: 0.5094 (m-30) REVERT: A 261 MET cc_start: 0.8243 (ttp) cc_final: 0.7576 (ttp) REVERT: A 322 MET cc_start: 0.9175 (tpt) cc_final: 0.8729 (tpt) REVERT: A 570 TYR cc_start: 0.7694 (p90) cc_final: 0.7339 (p90) REVERT: A 633 MET cc_start: 0.8853 (tpt) cc_final: 0.8053 (pmm) REVERT: A 640 LEU cc_start: 0.9212 (mt) cc_final: 0.8854 (pp) REVERT: A 664 LYS cc_start: 0.9264 (mmtm) cc_final: 0.8728 (mppt) REVERT: B 60 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 126 MET cc_start: 0.8431 (tmm) cc_final: 0.7906 (mtm) REVERT: D 61 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7763 (mmm-85) REVERT: D 107 LEU cc_start: 0.8604 (tp) cc_final: 0.8364 (tp) REVERT: D 115 TRP cc_start: 0.8506 (p-90) cc_final: 0.8111 (p-90) REVERT: D 133 ASP cc_start: 0.7528 (p0) cc_final: 0.6861 (t0) REVERT: D 140 MET cc_start: 0.8134 (mtm) cc_final: 0.7817 (mtt) REVERT: D 145 MET cc_start: 0.7949 (tmm) cc_final: 0.7399 (tmm) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.2215 time to fit residues: 48.1131 Evaluate side-chains 145 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 451 VAL Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 91 GLU 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 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.094307 restraints weight = 24281.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093596 restraints weight = 23346.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094046 restraints weight = 23268.719| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9716 Z= 0.216 Angle : 0.674 9.142 13132 Z= 0.341 Chirality : 0.043 0.206 1466 Planarity : 0.004 0.063 1685 Dihedral : 4.045 22.213 1267 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.37 % Allowed : 22.51 % Favored : 75.12 % 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: 0.45 (0.25), residues: 1165 helix: 1.18 (0.19), residues: 707 sheet: -2.73 (0.78), residues: 27 loop : -0.93 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 303 HIS 0.014 0.001 HIS C 309 PHE 0.029 0.002 PHE A 498 TYR 0.029 0.002 TYR A 278 ARG 0.004 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3380.58 seconds wall clock time: 63 minutes 26.97 seconds (3806.97 seconds total)