Starting phenix.real_space_refine on Fri Feb 14 22:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.map" model { file = "/net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r88_24311/02_2025/7r88_24311.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6964 2.51 5 N 1826 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10787 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4620 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 21, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4463 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 537} Chain breaks: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 6.66, per 1000 atoms: 0.62 Number of scatterers: 10787 At special positions: 0 Unit cell: (113.288, 108.29, 120.785, 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 66 16.00 O 1931 8.00 N 1826 7.00 C 6964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 52.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.270A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 313 through 331 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.908A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 402 removed outlier: 5.359A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.213A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.676A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.647A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.270A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 614 through 617 removed outlier: 4.351A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 619 through 649 removed outlier: 4.258A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 4.430A pdb=" N HIS A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.674A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 316 through 325 removed outlier: 4.050A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.512A pdb=" N GLU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 458 through 473 removed outlier: 4.488A pdb=" N ASN B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 3.515A pdb=" N GLY B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 517 removed outlier: 4.005A pdb=" N PHE B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix removed outlier: 4.352A pdb=" N TRP B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.603A pdb=" N TRP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.971A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 6.876A pdb=" N LYS A 70 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 44 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 72 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 43 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 110 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.441A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.595A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.730A pdb=" N GLY B 105 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.182A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.479A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 2.88 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: 3433 1.34 - 1.46: 2498 1.46 - 1.58: 4985 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 11021 Sorted by residual: bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.50e+00 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.44e-02 4.82e+03 1.07e+00 bond pdb=" C ASN A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.44e-02 4.82e+03 8.22e-01 bond pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.70e-01 bond pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.21e-01 ... (remaining 11016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14735 1.55 - 3.10: 144 3.10 - 4.65: 28 4.65 - 6.20: 10 6.20 - 7.75: 1 Bond angle restraints: 14918 Sorted by residual: angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N SER B 581 " pdb=" CA SER B 581 " pdb=" C SER B 581 " ideal model delta sigma weight residual 114.56 110.78 3.78 1.27e+00 6.20e-01 8.84e+00 angle pdb=" N VAL A 180 " pdb=" CA VAL A 180 " pdb=" C VAL A 180 " ideal model delta sigma weight residual 111.88 109.23 2.65 1.06e+00 8.90e-01 6.27e+00 angle pdb=" N PHE A 442 " pdb=" CA PHE A 442 " pdb=" C PHE A 442 " ideal model delta sigma weight residual 109.81 115.06 -5.25 2.21e+00 2.05e-01 5.64e+00 angle pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta sigma weight residual 110.49 114.26 -3.77 1.69e+00 3.50e-01 4.99e+00 ... (remaining 14913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6060 17.97 - 35.95: 406 35.95 - 53.92: 74 53.92 - 71.90: 8 71.90 - 89.87: 7 Dihedral angle restraints: 6555 sinusoidal: 2605 harmonic: 3950 Sorted by residual: dihedral pdb=" CB CYS A 587 " pdb=" SG CYS A 587 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual -86.00 -46.38 -39.62 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA CYS A 600 " pdb=" C CYS A 600 " pdb=" N ALA A 601 " pdb=" CA ALA A 601 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1301 0.038 - 0.076: 299 0.076 - 0.114: 84 0.114 - 0.152: 11 0.152 - 0.190: 2 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL B 210 " pdb=" N VAL B 210 " pdb=" C VAL B 210 " pdb=" CB VAL B 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1694 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 488 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C THR B 488 " -0.020 2.00e-02 2.50e+03 pdb=" O THR B 488 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 489 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 555 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 556 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " 0.015 5.00e-02 4.00e+02 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2777 2.80 - 3.32: 9800 3.32 - 3.85: 17768 3.85 - 4.37: 19939 4.37 - 4.90: 36069 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb=" OH TYR B 54 " pdb=" O GLY B 125 " model vdw 2.274 3.040 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.288 3.040 nonbonded pdb=" ND2 ASN A 551 " pdb=" OE1 GLU A 554 " model vdw 2.297 3.120 nonbonded pdb=" O ARG B 198 " pdb=" OG SER D 50 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR C 43 " pdb=" O ASN C 98 " model vdw 2.313 3.040 ... (remaining 86348 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: 1.110 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.002 0.037 11021 Z= 0.109 Angle : 0.454 7.753 14918 Z= 0.268 Chirality : 0.036 0.190 1697 Planarity : 0.003 0.033 1878 Dihedral : 12.488 89.872 4012 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.02 % Allowed : 5.76 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1348 helix: 0.30 (0.18), residues: 701 sheet: -1.30 (0.34), residues: 185 loop : -2.89 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 229 HIS 0.002 0.000 HIS B 531 PHE 0.006 0.001 PHE C 48 TYR 0.006 0.001 TYR C 115 ARG 0.001 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7407 (mtt180) REVERT: A 368 LEU cc_start: 0.8453 (tp) cc_final: 0.8240 (tp) REVERT: A 564 TYR cc_start: 0.8546 (m-80) cc_final: 0.8336 (m-80) REVERT: B 185 ASP cc_start: 0.7818 (m-30) cc_final: 0.7548 (m-30) REVERT: C 81 TYR cc_start: 0.8545 (m-80) cc_final: 0.8331 (m-80) REVERT: C 104 MET cc_start: 0.7995 (mtm) cc_final: 0.7688 (mtm) REVERT: D 99 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8084 (mp0) outliers start: 12 outliers final: 8 residues processed: 240 average time/residue: 0.2472 time to fit residues: 82.2952 Evaluate side-chains 180 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 206 GLN A 378 ASN A 392 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 510 HIS A 578 ASN A 604 GLN A 607 GLN B 99 GLN B 135 ASN B 153 GLN B 199 GLN B 270 HIS B 302 GLN B 409 ASN B 438 HIS B 462 ASN B 526 GLN B 568 ASN B 607 GLN C 75 ASN D 58 GLN D 65 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.081583 restraints weight = 16463.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.084780 restraints weight = 8550.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.086875 restraints weight = 5659.624| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11021 Z= 0.394 Angle : 0.673 10.339 14918 Z= 0.337 Chirality : 0.045 0.213 1697 Planarity : 0.004 0.043 1878 Dihedral : 4.560 47.979 1510 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.22 % Allowed : 11.44 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -0.34 (0.23), residues: 1348 helix: 1.22 (0.19), residues: 700 sheet: -1.14 (0.34), residues: 188 loop : -2.11 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 128 HIS 0.007 0.001 HIS A 510 PHE 0.023 0.002 PHE A 109 TYR 0.022 0.002 TYR B 507 ARG 0.004 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.232 Fit side-chains REVERT: A 324 MET cc_start: 0.8398 (tmm) cc_final: 0.8030 (tmm) REVERT: B 286 MET cc_start: 0.8960 (mmm) cc_final: 0.8170 (mtm) REVERT: B 571 TYR cc_start: 0.9159 (t80) cc_final: 0.8925 (t80) REVERT: D 31 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8145 (tt) outliers start: 38 outliers final: 21 residues processed: 180 average time/residue: 0.2132 time to fit residues: 56.4322 Evaluate side-chains 164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS D 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.085135 restraints weight = 16471.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.088390 restraints weight = 8528.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090566 restraints weight = 5633.174| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11021 Z= 0.187 Angle : 0.533 8.597 14918 Z= 0.264 Chirality : 0.040 0.189 1697 Planarity : 0.003 0.046 1878 Dihedral : 4.058 59.820 1501 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 14.32 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.30 (0.23), residues: 1348 helix: 1.75 (0.20), residues: 704 sheet: -0.90 (0.34), residues: 194 loop : -1.84 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS A 470 PHE 0.017 0.001 PHE A 109 TYR 0.020 0.001 TYR B 507 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.218 Fit side-chains REVERT: A 324 MET cc_start: 0.8400 (tmm) cc_final: 0.8041 (tmm) REVERT: A 552 ILE cc_start: 0.9139 (mt) cc_final: 0.8873 (pt) REVERT: B 286 MET cc_start: 0.8889 (mmm) cc_final: 0.8246 (mtm) REVERT: B 571 TYR cc_start: 0.9128 (t80) cc_final: 0.8903 (t80) REVERT: C 75 ASN cc_start: 0.9232 (m-40) cc_final: 0.8680 (m-40) REVERT: D 97 SER cc_start: 0.8686 (t) cc_final: 0.8347 (p) outliers start: 23 outliers final: 15 residues processed: 166 average time/residue: 0.2053 time to fit residues: 50.8547 Evaluate side-chains 154 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 90 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.082565 restraints weight = 16468.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085785 restraints weight = 8629.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087912 restraints weight = 5720.345| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11021 Z= 0.234 Angle : 0.539 8.658 14918 Z= 0.267 Chirality : 0.041 0.173 1697 Planarity : 0.003 0.045 1878 Dihedral : 3.797 51.491 1498 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.22 % Allowed : 14.66 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.69 (0.24), residues: 1348 helix: 1.99 (0.20), residues: 699 sheet: -0.44 (0.36), residues: 190 loop : -1.61 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.005 0.001 HIS A 470 PHE 0.014 0.001 PHE A 109 TYR 0.015 0.001 TYR B 507 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 324 MET cc_start: 0.8424 (tmm) cc_final: 0.8072 (tmm) REVERT: A 637 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7753 (tp) REVERT: B 286 MET cc_start: 0.8848 (mmm) cc_final: 0.8262 (mtm) REVERT: B 406 GLN cc_start: 0.8579 (tt0) cc_final: 0.8354 (tt0) REVERT: B 571 TYR cc_start: 0.9150 (t80) cc_final: 0.8938 (t80) REVERT: C 38 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7313 (mtp85) REVERT: C 75 ASN cc_start: 0.9237 (m-40) cc_final: 0.8676 (m-40) REVERT: C 103 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7992 (tp40) REVERT: D 90 ASP cc_start: 0.7841 (m-30) cc_final: 0.7507 (m-30) REVERT: D 97 SER cc_start: 0.8785 (t) cc_final: 0.8513 (p) outliers start: 38 outliers final: 24 residues processed: 167 average time/residue: 0.2069 time to fit residues: 51.7717 Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 111 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.083887 restraints weight = 16411.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.087135 restraints weight = 8566.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.089298 restraints weight = 5672.627| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11021 Z= 0.187 Angle : 0.518 8.348 14918 Z= 0.256 Chirality : 0.040 0.174 1697 Planarity : 0.003 0.046 1878 Dihedral : 3.729 49.745 1498 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.97 % Allowed : 15.51 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.93 (0.24), residues: 1348 helix: 2.14 (0.20), residues: 698 sheet: -0.19 (0.37), residues: 190 loop : -1.48 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.007 0.001 HIS A 493 PHE 0.014 0.001 PHE B 445 TYR 0.014 0.001 TYR B 507 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 302 MET cc_start: 0.8383 (tpp) cc_final: 0.8182 (mmm) REVERT: A 315 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 324 MET cc_start: 0.8426 (tmm) cc_final: 0.8072 (tmm) REVERT: A 630 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 637 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7686 (tp) REVERT: B 286 MET cc_start: 0.8800 (mmm) cc_final: 0.8216 (mtm) REVERT: B 406 GLN cc_start: 0.8597 (tt0) cc_final: 0.8386 (tt0) REVERT: B 582 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 628 LYS cc_start: 0.6676 (pmtt) cc_final: 0.6311 (pttp) REVERT: C 38 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7445 (mtp85) REVERT: C 75 ASN cc_start: 0.9237 (m-40) cc_final: 0.8675 (m-40) REVERT: C 103 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8003 (tp40) REVERT: D 31 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 97 SER cc_start: 0.8769 (t) cc_final: 0.8520 (p) outliers start: 35 outliers final: 26 residues processed: 165 average time/residue: 0.2172 time to fit residues: 53.7476 Evaluate side-chains 168 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.083003 restraints weight = 16647.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.086222 restraints weight = 8662.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.088371 restraints weight = 5733.366| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11021 Z= 0.209 Angle : 0.522 8.661 14918 Z= 0.259 Chirality : 0.040 0.171 1697 Planarity : 0.003 0.046 1878 Dihedral : 3.743 48.049 1498 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.64 % Allowed : 15.59 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1348 helix: 2.20 (0.20), residues: 700 sheet: -0.06 (0.37), residues: 190 loop : -1.31 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS A 470 PHE 0.015 0.001 PHE B 445 TYR 0.019 0.001 TYR D 111 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 302 MET cc_start: 0.8386 (tpp) cc_final: 0.8115 (mmm) REVERT: A 324 MET cc_start: 0.8418 (tmm) cc_final: 0.8084 (tmm) REVERT: A 625 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 630 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8305 (t80) REVERT: A 637 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7812 (tp) REVERT: B 286 MET cc_start: 0.8799 (mmm) cc_final: 0.8199 (mtm) REVERT: B 406 GLN cc_start: 0.8631 (tt0) cc_final: 0.8420 (tt0) REVERT: B 582 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 628 LYS cc_start: 0.6749 (pmtt) cc_final: 0.6411 (pttp) REVERT: C 38 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7609 (mtp85) REVERT: C 75 ASN cc_start: 0.9234 (m-40) cc_final: 0.8665 (m-40) REVERT: C 103 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8095 (tp40) REVERT: D 31 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (tt) REVERT: D 97 SER cc_start: 0.8792 (t) cc_final: 0.8587 (p) outliers start: 43 outliers final: 28 residues processed: 171 average time/residue: 0.2144 time to fit residues: 54.0688 Evaluate side-chains 170 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS B 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.079275 restraints weight = 16920.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.082432 restraints weight = 8809.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.084522 restraints weight = 5844.374| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11021 Z= 0.391 Angle : 0.625 10.598 14918 Z= 0.311 Chirality : 0.044 0.164 1697 Planarity : 0.004 0.046 1878 Dihedral : 4.150 54.437 1498 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.64 % Allowed : 16.36 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.85 (0.24), residues: 1348 helix: 1.94 (0.20), residues: 702 sheet: -0.14 (0.37), residues: 190 loop : -1.34 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 584 HIS 0.005 0.001 HIS A 470 PHE 0.016 0.002 PHE B 445 TYR 0.025 0.002 TYR D 111 ARG 0.004 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.8454 (tmm) cc_final: 0.8129 (tmm) REVERT: A 625 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 637 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8002 (tp) REVERT: B 286 MET cc_start: 0.8895 (mmm) cc_final: 0.8288 (mtm) REVERT: B 406 GLN cc_start: 0.8659 (tt0) cc_final: 0.8455 (tt0) REVERT: B 628 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6615 (pttp) REVERT: C 38 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7541 (mtp85) REVERT: C 103 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8057 (tp40) REVERT: D 31 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8265 (tt) REVERT: D 97 SER cc_start: 0.8885 (t) cc_final: 0.8650 (p) REVERT: D 114 TYR cc_start: 0.8850 (t80) cc_final: 0.8613 (t80) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 0.2070 time to fit residues: 50.5535 Evaluate side-chains 167 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 628 LYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 83 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.084106 restraints weight = 16418.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.087370 restraints weight = 8558.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089531 restraints weight = 5647.683| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11021 Z= 0.144 Angle : 0.535 8.778 14918 Z= 0.263 Chirality : 0.040 0.207 1697 Planarity : 0.003 0.047 1878 Dihedral : 3.879 51.796 1498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.71 % Allowed : 17.03 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1348 helix: 2.27 (0.20), residues: 697 sheet: -0.10 (0.37), residues: 194 loop : -1.21 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 461 HIS 0.006 0.001 HIS A 470 PHE 0.012 0.001 PHE A 109 TYR 0.014 0.001 TYR B 507 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 302 MET cc_start: 0.7910 (mmm) cc_final: 0.7241 (mtp) REVERT: A 324 MET cc_start: 0.8432 (tmm) cc_final: 0.8107 (tmm) REVERT: A 637 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 286 MET cc_start: 0.8790 (mmm) cc_final: 0.8190 (mtm) REVERT: B 406 GLN cc_start: 0.8617 (tt0) cc_final: 0.8415 (tt0) REVERT: B 628 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6599 (pttp) REVERT: C 38 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8070 (mtp85) REVERT: C 75 ASN cc_start: 0.9235 (m-40) cc_final: 0.8698 (m-40) outliers start: 32 outliers final: 23 residues processed: 161 average time/residue: 0.2147 time to fit residues: 50.6717 Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 628 LYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 122 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.083286 restraints weight = 16494.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086555 restraints weight = 8502.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088727 restraints weight = 5583.537| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11021 Z= 0.187 Angle : 0.548 9.345 14918 Z= 0.267 Chirality : 0.041 0.230 1697 Planarity : 0.003 0.046 1878 Dihedral : 3.820 50.282 1498 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.54 % Allowed : 17.54 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1348 helix: 2.34 (0.20), residues: 698 sheet: -0.03 (0.37), residues: 195 loop : -1.16 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.006 0.001 HIS A 470 PHE 0.013 0.001 PHE B 445 TYR 0.015 0.001 TYR D 111 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.8441 (tmm) cc_final: 0.8123 (tmm) REVERT: A 480 MET cc_start: 0.8455 (tpp) cc_final: 0.8245 (tpp) REVERT: B 286 MET cc_start: 0.8782 (mmm) cc_final: 0.8207 (mtm) REVERT: B 628 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6609 (pttp) REVERT: C 38 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8137 (mtp85) REVERT: C 75 ASN cc_start: 0.9232 (m-40) cc_final: 0.8669 (m-40) outliers start: 30 outliers final: 24 residues processed: 152 average time/residue: 0.2161 time to fit residues: 48.7732 Evaluate side-chains 158 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 628 LYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 91 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085223 restraints weight = 16429.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.088481 restraints weight = 8592.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090617 restraints weight = 5671.527| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11021 Z= 0.164 Angle : 0.545 11.937 14918 Z= 0.264 Chirality : 0.040 0.220 1697 Planarity : 0.003 0.046 1878 Dihedral : 3.795 52.318 1498 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.71 % Allowed : 17.63 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1348 helix: 2.38 (0.20), residues: 697 sheet: 0.12 (0.38), residues: 191 loop : -1.11 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 461 HIS 0.006 0.001 HIS A 470 PHE 0.012 0.001 PHE B 445 TYR 0.013 0.001 TYR B 507 ARG 0.003 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.199 Fit side-chains REVERT: A 166 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8675 (mtmm) REVERT: A 172 MET cc_start: 0.8090 (mtm) cc_final: 0.7757 (mtm) REVERT: A 324 MET cc_start: 0.8438 (tmm) cc_final: 0.8125 (tmm) REVERT: A 437 ASN cc_start: 0.8014 (m-40) cc_final: 0.7702 (m-40) REVERT: A 451 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 480 MET cc_start: 0.8460 (tpp) cc_final: 0.8252 (tpp) REVERT: A 506 LEU cc_start: 0.8962 (mt) cc_final: 0.8739 (mt) REVERT: A 637 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7688 (tt) REVERT: B 286 MET cc_start: 0.8763 (mmm) cc_final: 0.8204 (mtm) REVERT: B 628 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6556 (pttp) REVERT: C 38 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (mtp85) REVERT: C 75 ASN cc_start: 0.9226 (m-40) cc_final: 0.8648 (m-40) REVERT: D 24 MET cc_start: 0.8835 (mmm) cc_final: 0.8519 (tpt) outliers start: 32 outliers final: 25 residues processed: 157 average time/residue: 0.2150 time to fit residues: 49.8650 Evaluate side-chains 160 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 628 LYS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.104256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.081383 restraints weight = 16506.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.084556 restraints weight = 8653.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.086660 restraints weight = 5769.377| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11021 Z= 0.293 Angle : 0.594 9.902 14918 Z= 0.291 Chirality : 0.043 0.230 1697 Planarity : 0.003 0.046 1878 Dihedral : 3.957 50.235 1498 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.46 % Allowed : 17.37 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1348 helix: 2.20 (0.20), residues: 702 sheet: 0.15 (0.38), residues: 193 loop : -1.09 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.006 0.001 HIS A 470 PHE 0.013 0.001 PHE B 445 TYR 0.018 0.001 TYR D 111 ARG 0.003 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.54 seconds wall clock time: 54 minutes 6.83 seconds (3246.83 seconds total)