Starting phenix.real_space_refine on Sat Dec 28 20:53:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.map" model { file = "/net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gry_34217/12_2024/8gry_34217.cif" } resolution = 3.29 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4121 2.51 5 N 1076 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4872 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 28, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.77, per 1000 atoms: 1.05 Number of scatterers: 6444 At special positions: 0 Unit cell: (97.68, 76.56, 122.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1210 8.00 N 1076 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 937.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 53.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 3.808A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.582A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.523A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.973A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.749A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.503A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.196A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.992A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.513A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.518A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.626A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.022A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.751A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.506A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.645A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.657A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.990A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 294 hydrogen bonds defined for protein. 843 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: 1.74 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1147 1.33 - 1.45: 1861 1.45 - 1.57: 3561 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6625 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 1.469 1.430 0.039 1.28e-02 6.10e+03 9.20e+00 bond pdb=" C PRO B 499 " pdb=" O PRO B 499 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 5.97e+00 bond pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.42e-02 4.96e+03 2.02e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C2 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8771 1.56 - 3.12: 183 3.12 - 4.68: 42 4.68 - 6.24: 6 6.24 - 7.80: 1 Bond angle restraints: 9003 Sorted by residual: angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" C THR B 500 " ideal model delta sigma weight residual 114.64 106.84 7.80 1.52e+00 4.33e-01 2.63e+01 angle pdb=" N PRO B 499 " pdb=" CD PRO B 499 " pdb=" CG PRO B 499 " ideal model delta sigma weight residual 103.20 98.77 4.43 1.50e+00 4.44e-01 8.71e+00 angle pdb=" CA GLU A 182 " pdb=" CB GLU A 182 " pdb=" CG GLU A 182 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.73e+00 angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 118.74 3.91 1.66e+00 3.63e-01 5.55e+00 ... (remaining 8998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.39: 3544 19.39 - 38.78: 310 38.78 - 58.17: 55 58.17 - 77.56: 11 77.56 - 96.95: 18 Dihedral angle restraints: 3938 sinusoidal: 1609 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 158.94 -65.94 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 130.04 -37.04 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 3935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 719 0.042 - 0.084: 162 0.084 - 0.126: 53 0.126 - 0.169: 4 0.169 - 0.211: 3 Chirality restraints: 941 Sorted by residual: chirality pdb=" C2 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" C3 NAG B 601 " pdb=" N2 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.28 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C4 NAG B 601 " pdb=" C3 NAG B 601 " pdb=" C5 NAG B 601 " pdb=" O4 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 938 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO A 258 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C GLN A 89 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 90 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 182 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" CD GLU A 182 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 182 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 182 " -0.009 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 48 2.58 - 3.16: 5250 3.16 - 3.74: 9530 3.74 - 4.32: 12523 4.32 - 4.90: 21645 Nonbonded interactions: 48996 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 494 " pdb=" N GLU A 495 " model vdw 2.178 3.120 nonbonded pdb=" OG SER A 607 " pdb=" OD2 ASP A 609 " model vdw 2.234 3.040 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.278 3.040 nonbonded pdb=" NE1 TRP A 478 " pdb=" OD2 ASP A 499 " model vdw 2.286 3.120 ... (remaining 48991 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.280 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: 20.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 0.039 6625 Z= 0.165 Angle : 0.578 7.798 9003 Z= 0.315 Chirality : 0.041 0.211 941 Planarity : 0.004 0.069 1169 Dihedral : 16.151 96.951 2421 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % 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 (0.31), residues: 788 helix: 1.69 (0.29), residues: 367 sheet: 1.81 (0.92), residues: 39 loop : -1.35 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.004 0.001 HIS A 401 PHE 0.009 0.001 PHE A 592 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7319 (tp30) cc_final: 0.6860 (tp30) REVERT: A 77 SER cc_start: 0.8125 (t) cc_final: 0.7731 (p) REVERT: A 126 ILE cc_start: 0.8802 (tp) cc_final: 0.8517 (tt) REVERT: A 150 GLU cc_start: 0.6569 (pp20) cc_final: 0.6300 (tm-30) REVERT: A 313 LYS cc_start: 0.7795 (tttt) cc_final: 0.7534 (tmmt) REVERT: A 341 LYS cc_start: 0.7636 (mttp) cc_final: 0.7329 (mttp) REVERT: A 360 MET cc_start: 0.8291 (ttm) cc_final: 0.8077 (ttm) REVERT: A 376 MET cc_start: 0.7491 (tpp) cc_final: 0.7275 (ttp) REVERT: A 475 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7691 (ttpt) REVERT: A 517 THR cc_start: 0.6970 (p) cc_final: 0.6639 (p) REVERT: A 541 LYS cc_start: 0.6731 (mttt) cc_final: 0.6435 (mttt) REVERT: A 562 ASN cc_start: 0.7313 (t0) cc_final: 0.7037 (t0) REVERT: A 574 VAL cc_start: 0.8340 (m) cc_final: 0.8096 (p) REVERT: B 336 CYS cc_start: 0.4205 (m) cc_final: 0.3324 (m) REVERT: B 357 ARG cc_start: 0.6541 (ptm-80) cc_final: 0.6160 (ptm-80) REVERT: B 469 SER cc_start: 0.8276 (t) cc_final: 0.8068 (t) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2173 time to fit residues: 57.3954 Evaluate side-chains 181 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.0980 chunk 70 optimal weight: 0.0470 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6625 Z= 0.142 Angle : 0.551 9.725 9003 Z= 0.274 Chirality : 0.041 0.212 941 Planarity : 0.004 0.053 1169 Dihedral : 5.341 56.725 885 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.44 % Allowed : 8.78 % Favored : 89.78 % 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: 0.86 (0.31), residues: 788 helix: 2.02 (0.28), residues: 372 sheet: 1.87 (0.94), residues: 39 loop : -1.14 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 401 PHE 0.010 0.001 PHE A 592 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7335 (tp30) cc_final: 0.7014 (tp30) REVERT: A 126 ILE cc_start: 0.8810 (tp) cc_final: 0.8472 (tt) REVERT: A 181 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: A 182 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 197 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6444 (tm-30) REVERT: A 206 ASP cc_start: 0.7747 (t0) cc_final: 0.7478 (t0) REVERT: A 313 LYS cc_start: 0.7766 (tttt) cc_final: 0.7428 (ttmm) REVERT: A 341 LYS cc_start: 0.7676 (mttp) cc_final: 0.7385 (mttp) REVERT: A 347 THR cc_start: 0.7951 (m) cc_final: 0.7681 (p) REVERT: A 458 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7381 (tptm) REVERT: A 472 GLN cc_start: 0.7883 (mp10) cc_final: 0.7586 (mp10) REVERT: A 475 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7707 (ttpt) REVERT: A 476 LYS cc_start: 0.7794 (tppt) cc_final: 0.7559 (tppp) REVERT: A 482 ARG cc_start: 0.7132 (ttm170) cc_final: 0.6785 (ttm-80) REVERT: A 517 THR cc_start: 0.6899 (p) cc_final: 0.6493 (p) REVERT: A 557 MET cc_start: 0.7825 (tmm) cc_final: 0.7524 (ttp) REVERT: A 562 ASN cc_start: 0.7385 (t0) cc_final: 0.6957 (t0) REVERT: A 574 VAL cc_start: 0.8375 (m) cc_final: 0.8175 (p) REVERT: B 336 CYS cc_start: 0.4250 (m) cc_final: 0.3669 (m) REVERT: B 357 ARG cc_start: 0.6560 (ptm-80) cc_final: 0.6209 (ptm-80) REVERT: B 469 SER cc_start: 0.8472 (t) cc_final: 0.8121 (t) outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.2182 time to fit residues: 51.2232 Evaluate side-chains 176 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.0972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6625 Z= 0.145 Angle : 0.527 9.852 9003 Z= 0.263 Chirality : 0.041 0.240 941 Planarity : 0.004 0.046 1169 Dihedral : 4.919 54.296 885 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.44 % Allowed : 12.81 % Favored : 85.76 % 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: 0.89 (0.31), residues: 788 helix: 2.11 (0.29), residues: 366 sheet: 1.59 (0.91), residues: 41 loop : -1.12 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 401 PHE 0.013 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7362 (tp30) cc_final: 0.7040 (tp30) REVERT: A 77 SER cc_start: 0.8159 (t) cc_final: 0.7873 (m) REVERT: A 126 ILE cc_start: 0.8861 (tp) cc_final: 0.8496 (tt) REVERT: A 142 PHE cc_start: 0.6069 (m-10) cc_final: 0.5708 (m-10) REVERT: A 182 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7525 (pp20) REVERT: A 206 ASP cc_start: 0.7784 (t0) cc_final: 0.7558 (t0) REVERT: A 225 ASP cc_start: 0.6653 (m-30) cc_final: 0.6357 (m-30) REVERT: A 341 LYS cc_start: 0.7680 (mttp) cc_final: 0.7409 (mttp) REVERT: A 347 THR cc_start: 0.8135 (m) cc_final: 0.7654 (p) REVERT: A 358 ILE cc_start: 0.8448 (mt) cc_final: 0.7979 (tt) REVERT: A 475 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7696 (ttpt) REVERT: A 482 ARG cc_start: 0.7265 (ttm170) cc_final: 0.7019 (ttm-80) REVERT: A 557 MET cc_start: 0.7840 (tmm) cc_final: 0.7488 (ttp) REVERT: A 562 ASN cc_start: 0.7482 (t0) cc_final: 0.7226 (t0) REVERT: A 574 VAL cc_start: 0.8410 (m) cc_final: 0.8169 (p) REVERT: B 469 SER cc_start: 0.8455 (t) cc_final: 0.8254 (t) outliers start: 10 outliers final: 6 residues processed: 187 average time/residue: 0.2276 time to fit residues: 53.8753 Evaluate side-chains 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 0.0870 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6625 Z= 0.202 Angle : 0.568 9.725 9003 Z= 0.287 Chirality : 0.042 0.247 941 Planarity : 0.004 0.042 1169 Dihedral : 5.139 55.962 885 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.01 % Allowed : 14.53 % Favored : 83.45 % 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: 0.72 (0.31), residues: 788 helix: 2.06 (0.28), residues: 365 sheet: 0.58 (0.84), residues: 51 loop : -1.22 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.012 0.001 PHE A 592 TYR 0.028 0.001 TYR A 158 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7337 (tp30) cc_final: 0.7007 (tp30) REVERT: A 77 SER cc_start: 0.8223 (t) cc_final: 0.7941 (m) REVERT: A 126 ILE cc_start: 0.8952 (tp) cc_final: 0.8586 (tt) REVERT: A 152 MET cc_start: 0.7055 (mmm) cc_final: 0.6719 (mmm) REVERT: A 182 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7490 (pp20) REVERT: A 206 ASP cc_start: 0.7750 (t0) cc_final: 0.7463 (t0) REVERT: A 213 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7036 (mm-30) REVERT: A 225 ASP cc_start: 0.6799 (m-30) cc_final: 0.6482 (m-30) REVERT: A 359 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8076 (ttpp) REVERT: A 475 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7813 (ttpt) REVERT: A 482 ARG cc_start: 0.7367 (ttm170) cc_final: 0.7042 (ttm-80) REVERT: A 517 THR cc_start: 0.7054 (p) cc_final: 0.6764 (p) REVERT: A 557 MET cc_start: 0.7920 (tmm) cc_final: 0.7555 (ttp) REVERT: A 562 ASN cc_start: 0.7622 (t0) cc_final: 0.7245 (t0) REVERT: A 610 TRP cc_start: 0.8314 (t60) cc_final: 0.7944 (t60) REVERT: B 393 THR cc_start: 0.6956 (m) cc_final: 0.6621 (p) REVERT: B 469 SER cc_start: 0.8503 (t) cc_final: 0.8231 (t) REVERT: B 501 TYR cc_start: 0.7862 (m-10) cc_final: 0.7274 (m-10) outliers start: 14 outliers final: 10 residues processed: 188 average time/residue: 0.2253 time to fit residues: 53.2458 Evaluate side-chains 188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6625 Z= 0.314 Angle : 0.627 9.754 9003 Z= 0.322 Chirality : 0.044 0.256 941 Planarity : 0.004 0.043 1169 Dihedral : 5.368 55.643 885 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 16.40 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 788 helix: 1.87 (0.28), residues: 365 sheet: 0.84 (0.86), residues: 49 loop : -1.39 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.006 0.001 HIS A 374 PHE 0.020 0.002 PHE A 592 TYR 0.024 0.002 TYR A 158 ARG 0.016 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7300 (tp30) cc_final: 0.6968 (tp30) REVERT: A 113 ASN cc_start: 0.8687 (t0) cc_final: 0.8428 (t0) REVERT: A 126 ILE cc_start: 0.9032 (tp) cc_final: 0.8612 (tt) REVERT: A 152 MET cc_start: 0.6729 (mmm) cc_final: 0.6081 (tpp) REVERT: A 155 SER cc_start: 0.8788 (t) cc_final: 0.7570 (m) REVERT: A 206 ASP cc_start: 0.7717 (t0) cc_final: 0.7187 (t0) REVERT: A 213 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 225 ASP cc_start: 0.6892 (m-30) cc_final: 0.6518 (m-30) REVERT: A 250 GLU cc_start: 0.7807 (tp30) cc_final: 0.7533 (tm-30) REVERT: A 257 SER cc_start: 0.8483 (p) cc_final: 0.8076 (p) REVERT: A 475 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7886 (ttpt) REVERT: A 482 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7218 (ttm-80) REVERT: A 509 ASP cc_start: 0.8260 (t70) cc_final: 0.7914 (t70) REVERT: A 517 THR cc_start: 0.7120 (p) cc_final: 0.6820 (p) REVERT: A 557 MET cc_start: 0.7947 (tmm) cc_final: 0.7596 (ttp) REVERT: A 598 GLN cc_start: 0.7695 (tp40) cc_final: 0.7419 (tp40) REVERT: A 610 TRP cc_start: 0.8415 (t60) cc_final: 0.8034 (t60) REVERT: B 469 SER cc_start: 0.8603 (t) cc_final: 0.8371 (t) REVERT: B 501 TYR cc_start: 0.7977 (m-10) cc_final: 0.7553 (m-80) outliers start: 15 outliers final: 9 residues processed: 187 average time/residue: 0.2205 time to fit residues: 52.7517 Evaluate side-chains 188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 39 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6625 Z= 0.221 Angle : 0.601 9.610 9003 Z= 0.302 Chirality : 0.043 0.232 941 Planarity : 0.005 0.112 1169 Dihedral : 4.801 55.275 885 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.87 % Allowed : 16.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 788 helix: 1.90 (0.28), residues: 366 sheet: 0.75 (0.86), residues: 49 loop : -1.35 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE A 142 TYR 0.021 0.001 TYR A 158 ARG 0.009 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7308 (tp30) cc_final: 0.6987 (tp30) REVERT: A 77 SER cc_start: 0.8259 (t) cc_final: 0.8031 (m) REVERT: A 87 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7335 (tp30) REVERT: A 113 ASN cc_start: 0.8679 (t0) cc_final: 0.8413 (t0) REVERT: A 126 ILE cc_start: 0.8976 (tp) cc_final: 0.8590 (tt) REVERT: A 213 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 225 ASP cc_start: 0.6858 (m-30) cc_final: 0.6495 (m-30) REVERT: A 250 GLU cc_start: 0.7722 (tp30) cc_final: 0.7422 (tm-30) REVERT: A 323 MET cc_start: 0.7994 (mmp) cc_final: 0.7791 (mmm) REVERT: A 347 THR cc_start: 0.7952 (m) cc_final: 0.7674 (p) REVERT: A 375 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 475 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7840 (ttpt) REVERT: A 482 ARG cc_start: 0.7484 (ttm170) cc_final: 0.7224 (ttm-80) REVERT: A 509 ASP cc_start: 0.8219 (t70) cc_final: 0.7886 (t70) REVERT: A 517 THR cc_start: 0.7035 (p) cc_final: 0.6756 (p) REVERT: A 557 MET cc_start: 0.7881 (tmm) cc_final: 0.7552 (ttp) REVERT: B 466 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8060 (mtp85) REVERT: B 501 TYR cc_start: 0.7984 (m-10) cc_final: 0.7529 (m-80) outliers start: 13 outliers final: 10 residues processed: 183 average time/residue: 0.2098 time to fit residues: 49.1573 Evaluate side-chains 184 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 30 optimal weight: 0.0980 chunk 44 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6625 Z= 0.183 Angle : 0.590 9.626 9003 Z= 0.297 Chirality : 0.042 0.230 941 Planarity : 0.005 0.128 1169 Dihedral : 4.645 55.258 885 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.73 % Allowed : 17.41 % Favored : 79.86 % 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: 0.59 (0.31), residues: 788 helix: 1.96 (0.28), residues: 366 sheet: 0.70 (0.86), residues: 49 loop : -1.34 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE A 504 TYR 0.019 0.001 TYR A 158 ARG 0.006 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7327 (tp30) cc_final: 0.7004 (tp30) REVERT: A 77 SER cc_start: 0.8264 (t) cc_final: 0.7985 (m) REVERT: A 87 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7349 (tp30) REVERT: A 119 ILE cc_start: 0.8377 (pt) cc_final: 0.8042 (mt) REVERT: A 126 ILE cc_start: 0.8937 (tp) cc_final: 0.8700 (tp) REVERT: A 213 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7139 (mm-30) REVERT: A 225 ASP cc_start: 0.6816 (m-30) cc_final: 0.6440 (m-30) REVERT: A 250 GLU cc_start: 0.7684 (tp30) cc_final: 0.7327 (tm-30) REVERT: A 313 LYS cc_start: 0.7854 (tttm) cc_final: 0.7436 (ttmm) REVERT: A 375 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 475 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7816 (ttpt) REVERT: A 482 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7235 (ttm-80) REVERT: A 557 MET cc_start: 0.7853 (tmm) cc_final: 0.7522 (ttp) REVERT: A 598 GLN cc_start: 0.7809 (tp40) cc_final: 0.7557 (tp40) REVERT: B 501 TYR cc_start: 0.7967 (m-10) cc_final: 0.7549 (m-80) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.1943 time to fit residues: 43.7607 Evaluate side-chains 169 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 0.0020 chunk 59 optimal weight: 0.0270 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 overall best weight: 0.0652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6625 Z= 0.157 Angle : 0.598 9.830 9003 Z= 0.293 Chirality : 0.041 0.227 941 Planarity : 0.004 0.062 1169 Dihedral : 4.416 55.244 885 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.73 % Allowed : 18.56 % Favored : 79.71 % 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: 0.65 (0.31), residues: 788 helix: 2.02 (0.28), residues: 367 sheet: 0.48 (0.84), residues: 49 loop : -1.29 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.002 0.001 HIS A 373 PHE 0.015 0.001 PHE A 142 TYR 0.018 0.001 TYR A 385 ARG 0.008 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7920 (m-40) cc_final: 0.7689 (m-40) REVERT: A 75 GLU cc_start: 0.7347 (tp30) cc_final: 0.7022 (tp30) REVERT: A 77 SER cc_start: 0.8245 (t) cc_final: 0.7940 (m) REVERT: A 87 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7276 (tp30) REVERT: A 119 ILE cc_start: 0.8318 (pt) cc_final: 0.8023 (mt) REVERT: A 126 ILE cc_start: 0.8894 (tp) cc_final: 0.8646 (tp) REVERT: A 181 GLU cc_start: 0.7740 (tt0) cc_final: 0.7446 (mm-30) REVERT: A 207 TYR cc_start: 0.7834 (m-80) cc_final: 0.7608 (m-80) REVERT: A 213 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 225 ASP cc_start: 0.6783 (m-30) cc_final: 0.6478 (m-30) REVERT: A 250 GLU cc_start: 0.7613 (tp30) cc_final: 0.7200 (tm-30) REVERT: A 313 LYS cc_start: 0.7831 (tttm) cc_final: 0.7468 (ttmm) REVERT: A 341 LYS cc_start: 0.7707 (mttp) cc_final: 0.7487 (mttm) REVERT: A 475 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7816 (ttpt) REVERT: A 482 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7287 (ttm-80) REVERT: A 557 MET cc_start: 0.7861 (tmm) cc_final: 0.7446 (ttp) REVERT: A 563 SER cc_start: 0.8649 (t) cc_final: 0.8145 (p) REVERT: A 598 GLN cc_start: 0.7843 (tp40) cc_final: 0.7570 (tp40) REVERT: B 501 TYR cc_start: 0.7868 (m-10) cc_final: 0.7432 (m-80) outliers start: 12 outliers final: 8 residues processed: 164 average time/residue: 0.2063 time to fit residues: 44.1809 Evaluate side-chains 162 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 0.0170 chunk 35 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 562 ASN B 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6625 Z= 0.204 Angle : 0.605 9.651 9003 Z= 0.303 Chirality : 0.042 0.237 941 Planarity : 0.005 0.097 1169 Dihedral : 4.516 55.480 885 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.87 % Allowed : 19.14 % Favored : 78.99 % 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 (0.31), residues: 788 helix: 2.00 (0.28), residues: 367 sheet: 0.52 (0.84), residues: 49 loop : -1.28 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 504 TYR 0.018 0.001 TYR A 385 ARG 0.008 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7947 (m-40) cc_final: 0.7641 (m-40) REVERT: A 75 GLU cc_start: 0.7324 (tp30) cc_final: 0.6991 (tp30) REVERT: A 77 SER cc_start: 0.8263 (t) cc_final: 0.7994 (m) REVERT: A 87 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7355 (tp30) REVERT: A 119 ILE cc_start: 0.8413 (pt) cc_final: 0.8089 (mt) REVERT: A 126 ILE cc_start: 0.8921 (tp) cc_final: 0.8656 (tp) REVERT: A 165 TRP cc_start: 0.7595 (t60) cc_final: 0.7301 (t60) REVERT: A 181 GLU cc_start: 0.7775 (tt0) cc_final: 0.7510 (mm-30) REVERT: A 207 TYR cc_start: 0.7873 (m-80) cc_final: 0.7650 (m-80) REVERT: A 213 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7151 (mm-30) REVERT: A 225 ASP cc_start: 0.6822 (m-30) cc_final: 0.6527 (m-30) REVERT: A 250 GLU cc_start: 0.7663 (tp30) cc_final: 0.7242 (tm-30) REVERT: A 313 LYS cc_start: 0.7852 (tttm) cc_final: 0.7488 (ttmm) REVERT: A 341 LYS cc_start: 0.7715 (mttp) cc_final: 0.7472 (mttm) REVERT: A 347 THR cc_start: 0.7898 (m) cc_final: 0.7594 (p) REVERT: A 475 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7865 (ttpt) REVERT: A 482 ARG cc_start: 0.7555 (ttm170) cc_final: 0.7324 (ttm-80) REVERT: A 557 MET cc_start: 0.7894 (tmm) cc_final: 0.7482 (ttp) REVERT: A 563 SER cc_start: 0.8737 (t) cc_final: 0.8178 (p) REVERT: B 501 TYR cc_start: 0.7934 (m-10) cc_final: 0.7542 (m-80) outliers start: 13 outliers final: 8 residues processed: 170 average time/residue: 0.1929 time to fit residues: 43.0029 Evaluate side-chains 167 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6625 Z= 0.186 Angle : 0.602 9.636 9003 Z= 0.300 Chirality : 0.042 0.233 941 Planarity : 0.005 0.113 1169 Dihedral : 4.505 55.360 885 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.15 % Allowed : 19.57 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.31), residues: 788 helix: 1.99 (0.28), residues: 366 sheet: 0.52 (0.84), residues: 49 loop : -1.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE A 142 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7981 (m-40) cc_final: 0.7658 (m-40) REVERT: A 75 GLU cc_start: 0.7320 (tp30) cc_final: 0.6989 (tp30) REVERT: A 77 SER cc_start: 0.8274 (t) cc_final: 0.7999 (m) REVERT: A 119 ILE cc_start: 0.8398 (pt) cc_final: 0.8068 (mt) REVERT: A 126 ILE cc_start: 0.8913 (tp) cc_final: 0.8644 (tp) REVERT: A 165 TRP cc_start: 0.7543 (t60) cc_final: 0.7286 (t60) REVERT: A 207 TYR cc_start: 0.7848 (m-80) cc_final: 0.7619 (m-80) REVERT: A 213 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 225 ASP cc_start: 0.6826 (m-30) cc_final: 0.6517 (m-30) REVERT: A 250 GLU cc_start: 0.7623 (tp30) cc_final: 0.7209 (tm-30) REVERT: A 313 LYS cc_start: 0.7848 (tttm) cc_final: 0.7484 (ttmm) REVERT: A 341 LYS cc_start: 0.7680 (mttp) cc_final: 0.7449 (mttm) REVERT: A 347 THR cc_start: 0.7914 (m) cc_final: 0.7583 (p) REVERT: A 475 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7848 (ttpt) REVERT: A 482 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7296 (ttm-80) REVERT: A 557 MET cc_start: 0.7882 (tmm) cc_final: 0.7459 (ttp) REVERT: A 563 SER cc_start: 0.8718 (t) cc_final: 0.8166 (p) REVERT: B 501 TYR cc_start: 0.7925 (m-10) cc_final: 0.7516 (m-80) outliers start: 8 outliers final: 7 residues processed: 161 average time/residue: 0.1944 time to fit residues: 40.7587 Evaluate side-chains 164 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.0030 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113627 restraints weight = 9964.547| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.35 r_work: 0.3391 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6625 Z= 0.184 Angle : 0.601 9.631 9003 Z= 0.301 Chirality : 0.042 0.232 941 Planarity : 0.005 0.097 1169 Dihedral : 4.533 55.383 885 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.29 % Allowed : 19.71 % Favored : 78.99 % 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: 0.57 (0.31), residues: 788 helix: 1.97 (0.28), residues: 367 sheet: 0.28 (0.81), residues: 51 loop : -1.33 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE A 83 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.03 seconds wall clock time: 45 minutes 25.46 seconds (2725.46 seconds total)