Starting phenix.real_space_refine on Thu Mar 13 18:19:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gry_34217/03_2025/8gry_34217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gry_34217/03_2025/8gry_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_34217/03_2025/8gry_34217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gry_34217/03_2025/8gry_34217.map" model { file = "/net/cci-nas-00/data/ceres_data/8gry_34217/03_2025/8gry_34217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gry_34217/03_2025/8gry_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.14, per 1000 atoms: 1.11 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: 1.53 Conformation dependent library (CDL) restraints added in 982.3 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: 0.62 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: 1.60 Time building geometry restraints manager: 1.85 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: 12.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- 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 : 0.637 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: 0.2335 time to fit residues: 62.9283 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 : 0.852 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122909 restraints weight = 10115.385| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.48 r_work: 0.3475 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7798 (tp30) cc_final: 0.7389 (tp30) REVERT: A 126 ILE cc_start: 0.8878 (tp) cc_final: 0.8545 (tt) REVERT: A 150 GLU cc_start: 0.6816 (pp20) cc_final: 0.6588 (tm-30) REVERT: A 181 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 182 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 197 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 206 ASP cc_start: 0.8135 (t0) cc_final: 0.7858 (t0) REVERT: A 313 LYS cc_start: 0.7896 (tttt) cc_final: 0.7540 (ttmm) REVERT: A 341 LYS cc_start: 0.7952 (mttp) cc_final: 0.7668 (mttp) REVERT: A 347 THR cc_start: 0.8285 (m) cc_final: 0.7976 (p) REVERT: A 472 GLN cc_start: 0.8012 (mp10) cc_final: 0.7730 (mp10) REVERT: A 475 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7969 (ttpt) REVERT: A 476 LYS cc_start: 0.8085 (tppt) cc_final: 0.7850 (tppp) REVERT: A 482 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7317 (ttm-80) REVERT: A 517 THR cc_start: 0.7286 (p) cc_final: 0.6900 (p) REVERT: A 557 MET cc_start: 0.8301 (tmm) cc_final: 0.7965 (ttp) REVERT: A 562 ASN cc_start: 0.7643 (t0) cc_final: 0.7230 (t0) REVERT: A 574 VAL cc_start: 0.8335 (m) cc_final: 0.8124 (p) REVERT: B 336 CYS cc_start: 0.5510 (m) cc_final: 0.4954 (m) REVERT: B 357 ARG cc_start: 0.6979 (ptm-80) cc_final: 0.6629 (ptm-80) REVERT: B 469 SER cc_start: 0.8513 (t) cc_final: 0.8138 (t) REVERT: B 515 PHE cc_start: 0.7943 (m-80) cc_final: 0.7722 (m-80) outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.2099 time to fit residues: 49.3270 Evaluate side-chains 175 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 64 optimal weight: 0.0570 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116633 restraints weight = 10075.929| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.46 r_work: 0.3380 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6625 Z= 0.214 Angle : 0.563 9.960 9003 Z= 0.287 Chirality : 0.043 0.260 941 Planarity : 0.004 0.048 1169 Dihedral : 5.177 54.593 885 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.44 % Allowed : 12.66 % Favored : 85.90 % 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: 0.76 (0.31), residues: 788 helix: 2.04 (0.28), residues: 367 sheet: 0.77 (0.86), residues: 49 loop : -1.18 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.014 0.001 PHE A 592 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.001 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 196 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7837 (tp30) cc_final: 0.7410 (tp30) REVERT: A 77 SER cc_start: 0.8343 (t) cc_final: 0.8073 (m) REVERT: A 126 ILE cc_start: 0.9011 (tp) cc_final: 0.8648 (tt) REVERT: A 181 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: A 182 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7848 (pp20) REVERT: A 206 ASP cc_start: 0.8099 (t0) cc_final: 0.7812 (t0) REVERT: A 213 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 225 ASP cc_start: 0.7155 (m-30) cc_final: 0.6799 (m-30) REVERT: A 250 GLU cc_start: 0.8232 (tp30) cc_final: 0.8017 (tp30) REVERT: A 347 THR cc_start: 0.8414 (m) cc_final: 0.7930 (p) REVERT: A 462 MET cc_start: 0.8449 (mtp) cc_final: 0.8190 (mtm) REVERT: A 475 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8125 (ttpt) REVERT: A 482 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7607 (ttm-80) REVERT: A 517 THR cc_start: 0.7481 (p) cc_final: 0.7254 (p) REVERT: A 557 MET cc_start: 0.8365 (tmm) cc_final: 0.7998 (ttp) REVERT: A 562 ASN cc_start: 0.7792 (t0) cc_final: 0.7407 (t0) REVERT: A 610 TRP cc_start: 0.8424 (t60) cc_final: 0.8057 (t60) REVERT: B 357 ARG cc_start: 0.7041 (ptm-80) cc_final: 0.6664 (ptm-80) REVERT: B 393 THR cc_start: 0.7092 (m) cc_final: 0.6747 (p) REVERT: B 469 SER cc_start: 0.8515 (t) cc_final: 0.8227 (t) outliers start: 10 outliers final: 8 residues processed: 190 average time/residue: 0.2126 time to fit residues: 51.2035 Evaluate side-chains 192 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 181 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 363 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 5 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.0070 chunk 76 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 8 optimal weight: 0.0870 overall best weight: 0.0976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 86 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 = 0.3705 r_free = 0.3705 target = 0.129181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116591 restraints weight = 10165.890| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.44 r_work: 0.3443 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6625 Z= 0.151 Angle : 0.550 9.650 9003 Z= 0.274 Chirality : 0.041 0.233 941 Planarity : 0.004 0.065 1169 Dihedral : 5.134 55.338 885 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.44 % Allowed : 15.68 % Favored : 82.88 % 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: 0.76 (0.31), residues: 788 helix: 2.06 (0.28), residues: 365 sheet: 0.53 (0.83), residues: 51 loop : -1.17 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.009 0.001 PHE A 369 TYR 0.025 0.001 TYR A 158 ARG 0.004 0.000 ARG A 192 *********************** 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 182 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7813 (tp30) cc_final: 0.7399 (tp30) REVERT: A 77 SER cc_start: 0.8347 (t) cc_final: 0.8063 (m) REVERT: A 126 ILE cc_start: 0.8978 (tp) cc_final: 0.8596 (tt) REVERT: A 151 ILE cc_start: 0.6060 (tp) cc_final: 0.5594 (tp) REVERT: A 160 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6597 (ttt90) REVERT: A 182 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7837 (pp20) REVERT: A 206 ASP cc_start: 0.8178 (t0) cc_final: 0.7909 (t0) REVERT: A 213 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 225 ASP cc_start: 0.7140 (m-30) cc_final: 0.6821 (m-30) REVERT: A 250 GLU cc_start: 0.8191 (tp30) cc_final: 0.7897 (tm-30) REVERT: A 462 MET cc_start: 0.8397 (mtp) cc_final: 0.8138 (mtm) REVERT: A 475 LYS cc_start: 0.8221 (ttpt) cc_final: 0.8000 (ttpt) REVERT: A 482 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7545 (ttm-80) REVERT: A 517 THR cc_start: 0.7335 (p) cc_final: 0.6958 (p) REVERT: A 557 MET cc_start: 0.8317 (tmm) cc_final: 0.7904 (ttp) REVERT: A 610 TRP cc_start: 0.8332 (t60) cc_final: 0.7910 (t60) REVERT: B 350 VAL cc_start: 0.8312 (t) cc_final: 0.7178 (m) REVERT: B 357 ARG cc_start: 0.6982 (ptm-80) cc_final: 0.6609 (ptm-80) REVERT: B 393 THR cc_start: 0.7080 (m) cc_final: 0.6713 (p) REVERT: B 469 SER cc_start: 0.8533 (t) cc_final: 0.8312 (t) outliers start: 10 outliers final: 9 residues processed: 176 average time/residue: 0.2144 time to fit residues: 48.1600 Evaluate side-chains 183 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 543 ASP 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 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 59 optimal weight: 0.0670 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112404 restraints weight = 10069.799| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.38 r_work: 0.3370 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6625 Z= 0.228 Angle : 0.575 9.660 9003 Z= 0.290 Chirality : 0.043 0.249 941 Planarity : 0.004 0.055 1169 Dihedral : 4.753 55.736 885 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.87 % Allowed : 15.68 % Favored : 82.45 % 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: 0.63 (0.31), residues: 788 helix: 2.02 (0.28), residues: 364 sheet: 0.74 (0.86), residues: 49 loop : -1.33 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE A 592 TYR 0.021 0.001 TYR A 158 ARG 0.002 0.000 ARG A 192 *********************** 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 191 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8124 (tp30) cc_final: 0.7676 (tp30) REVERT: A 77 SER cc_start: 0.8486 (t) cc_final: 0.8231 (m) REVERT: A 87 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7813 (tp30) REVERT: A 126 ILE cc_start: 0.9109 (tp) cc_final: 0.8741 (tt) REVERT: A 151 ILE cc_start: 0.6256 (tp) cc_final: 0.5875 (tp) REVERT: A 160 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6947 (ttt90) REVERT: A 182 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8010 (pp20) REVERT: A 206 ASP cc_start: 0.8337 (t0) cc_final: 0.7944 (t0) REVERT: A 213 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 225 ASP cc_start: 0.7464 (m-30) cc_final: 0.7093 (m-30) REVERT: A 250 GLU cc_start: 0.8439 (tp30) cc_final: 0.8123 (tm-30) REVERT: A 269 ASP cc_start: 0.7887 (t0) cc_final: 0.7678 (t0) REVERT: A 419 LYS cc_start: 0.7566 (tptp) cc_final: 0.7348 (tptp) REVERT: A 482 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7942 (ttm-80) REVERT: A 509 ASP cc_start: 0.8713 (t0) cc_final: 0.8469 (t70) REVERT: A 517 THR cc_start: 0.7643 (p) cc_final: 0.7354 (p) REVERT: A 557 MET cc_start: 0.8504 (tmm) cc_final: 0.8097 (ttp) REVERT: A 610 TRP cc_start: 0.8503 (t60) cc_final: 0.7988 (t60) REVERT: B 357 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.7067 (ptm-80) REVERT: B 466 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8162 (mtp85) REVERT: B 469 SER cc_start: 0.8589 (t) cc_final: 0.8350 (t) REVERT: B 501 TYR cc_start: 0.8271 (m-10) cc_final: 0.7902 (m-80) outliers start: 13 outliers final: 9 residues processed: 184 average time/residue: 0.2155 time to fit residues: 50.4561 Evaluate side-chains 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 186 LEU Chi-restraints excluded: chain A residue 231 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 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 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.0270 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114050 restraints weight = 9926.770| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.30 r_work: 0.3340 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6625 Z= 0.276 Angle : 0.611 9.693 9003 Z= 0.311 Chirality : 0.044 0.245 941 Planarity : 0.004 0.048 1169 Dihedral : 4.884 55.462 885 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 16.98 % Favored : 81.01 % 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: 0.49 (0.30), residues: 788 helix: 1.93 (0.28), residues: 364 sheet: 0.69 (0.86), residues: 49 loop : -1.44 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.002 PHE A 592 TYR 0.019 0.002 TYR A 158 ARG 0.003 0.001 ARG A 192 *********************** 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 193 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8091 (tp30) cc_final: 0.7641 (tp30) REVERT: A 77 SER cc_start: 0.8515 (t) cc_final: 0.8287 (m) REVERT: A 87 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7834 (tp30) REVERT: A 126 ILE cc_start: 0.9091 (tp) cc_final: 0.8717 (tt) REVERT: A 151 ILE cc_start: 0.6442 (tp) cc_final: 0.6169 (tp) REVERT: A 182 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7996 (pp20) REVERT: A 206 ASP cc_start: 0.8360 (t0) cc_final: 0.8000 (t0) REVERT: A 213 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 225 ASP cc_start: 0.7495 (m-30) cc_final: 0.7112 (m-30) REVERT: A 250 GLU cc_start: 0.8372 (tp30) cc_final: 0.8141 (tp30) REVERT: A 313 LYS cc_start: 0.8098 (tttm) cc_final: 0.7620 (ttmm) REVERT: A 347 THR cc_start: 0.8414 (m) cc_final: 0.8062 (p) REVERT: A 358 ILE cc_start: 0.8728 (mt) cc_final: 0.8389 (tt) REVERT: A 476 LYS cc_start: 0.8384 (tppt) cc_final: 0.8136 (tppp) REVERT: A 482 ARG cc_start: 0.8223 (ttm170) cc_final: 0.8003 (ttm-80) REVERT: A 509 ASP cc_start: 0.8730 (t0) cc_final: 0.8401 (t70) REVERT: A 517 THR cc_start: 0.7611 (p) cc_final: 0.7335 (p) REVERT: A 557 MET cc_start: 0.8498 (tmm) cc_final: 0.8118 (ttp) REVERT: B 357 ARG cc_start: 0.7281 (ptm-80) cc_final: 0.6900 (ptm-80) REVERT: B 466 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8321 (mtp85) REVERT: B 469 SER cc_start: 0.8605 (t) cc_final: 0.8399 (t) REVERT: B 501 TYR cc_start: 0.8296 (m-10) cc_final: 0.7937 (m-80) outliers start: 14 outliers final: 11 residues processed: 184 average time/residue: 0.2404 time to fit residues: 58.0642 Evaluate side-chains 184 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 145 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 A residue 574 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 59 optimal weight: 0.0010 chunk 74 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.2082 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112380 restraints weight = 10074.092| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.40 r_work: 0.3369 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3368 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= 0.194 Angle : 0.591 9.658 9003 Z= 0.293 Chirality : 0.042 0.233 941 Planarity : 0.004 0.039 1169 Dihedral : 4.681 55.201 885 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.45 % Allowed : 17.27 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.30), residues: 788 helix: 1.92 (0.28), residues: 367 sheet: 0.64 (0.84), residues: 49 loop : -1.41 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE B 456 TYR 0.018 0.001 TYR A 158 ARG 0.007 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 188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8104 (tp30) cc_final: 0.7663 (tp30) REVERT: A 77 SER cc_start: 0.8502 (t) cc_final: 0.8242 (m) REVERT: A 87 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7822 (tp30) REVERT: A 126 ILE cc_start: 0.9076 (tp) cc_final: 0.8712 (tt) REVERT: A 160 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7331 (ttp80) REVERT: A 181 GLU cc_start: 0.8246 (tt0) cc_final: 0.7953 (mm-30) REVERT: A 182 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8029 (pp20) REVERT: A 206 ASP cc_start: 0.8418 (t0) cc_final: 0.8073 (t0) REVERT: A 213 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 225 ASP cc_start: 0.7481 (m-30) cc_final: 0.7107 (m-30) REVERT: A 250 GLU cc_start: 0.8367 (tp30) cc_final: 0.8020 (tm-30) REVERT: A 313 LYS cc_start: 0.8073 (tttm) cc_final: 0.7578 (ttmm) REVERT: A 358 ILE cc_start: 0.8733 (mt) cc_final: 0.8399 (tt) REVERT: A 476 LYS cc_start: 0.8324 (tppt) cc_final: 0.8077 (tppp) REVERT: A 482 ARG cc_start: 0.8232 (ttm170) cc_final: 0.8021 (ttm-80) REVERT: A 509 ASP cc_start: 0.8747 (t0) cc_final: 0.8495 (t70) REVERT: A 517 THR cc_start: 0.7625 (p) cc_final: 0.7314 (p) REVERT: A 557 MET cc_start: 0.8515 (tmm) cc_final: 0.8058 (ttp) REVERT: A 563 SER cc_start: 0.8747 (t) cc_final: 0.8239 (p) REVERT: B 357 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6880 (ptm-80) REVERT: B 501 TYR cc_start: 0.8287 (m-10) cc_final: 0.7889 (m-80) outliers start: 17 outliers final: 14 residues processed: 179 average time/residue: 0.2027 time to fit residues: 47.2235 Evaluate side-chains 183 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 145 GLU 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 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 361 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 64 optimal weight: 0.0010 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 0.0870 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 overall best weight: 0.1964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112780 restraints weight = 10093.290| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.40 r_work: 0.3371 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3472 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= 0.187 Angle : 0.583 9.643 9003 Z= 0.293 Chirality : 0.042 0.233 941 Planarity : 0.004 0.053 1169 Dihedral : 4.671 55.350 885 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.01 % Allowed : 17.12 % Favored : 80.86 % 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: 0.58 (0.30), residues: 788 helix: 1.98 (0.28), residues: 367 sheet: 0.61 (0.84), residues: 49 loop : -1.37 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 142 TYR 0.017 0.001 TYR A 385 ARG 0.007 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 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8103 (tp30) cc_final: 0.7657 (tp30) REVERT: A 77 SER cc_start: 0.8499 (t) cc_final: 0.8233 (m) REVERT: A 87 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7820 (tp30) REVERT: A 126 ILE cc_start: 0.9071 (tp) cc_final: 0.8717 (tt) REVERT: A 181 GLU cc_start: 0.8203 (tt0) cc_final: 0.7918 (mm-30) REVERT: A 182 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8000 (pp20) REVERT: A 206 ASP cc_start: 0.8385 (t0) cc_final: 0.8019 (t0) REVERT: A 213 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 225 ASP cc_start: 0.7480 (m-30) cc_final: 0.7144 (m-30) REVERT: A 250 GLU cc_start: 0.8338 (tp30) cc_final: 0.7960 (tm-30) REVERT: A 313 LYS cc_start: 0.8076 (tttm) cc_final: 0.7588 (ttmm) REVERT: A 358 ILE cc_start: 0.8717 (mt) cc_final: 0.8363 (tt) REVERT: A 476 LYS cc_start: 0.8332 (tppt) cc_final: 0.8092 (tppp) REVERT: A 482 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7999 (ttm-80) REVERT: A 509 ASP cc_start: 0.8725 (t0) cc_final: 0.8479 (t70) REVERT: A 557 MET cc_start: 0.8504 (tmm) cc_final: 0.8039 (ttp) REVERT: A 562 ASN cc_start: 0.7987 (t0) cc_final: 0.7576 (t0) REVERT: A 563 SER cc_start: 0.8765 (t) cc_final: 0.8253 (p) REVERT: B 501 TYR cc_start: 0.8274 (m-10) cc_final: 0.7905 (m-80) outliers start: 14 outliers final: 12 residues processed: 174 average time/residue: 0.1895 time to fit residues: 43.2223 Evaluate side-chains 177 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 186 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 48 optimal weight: 0.0050 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 4 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 overall best weight: 0.1092 ------------------------------------------------------------------------------- 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 B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117803 restraints weight = 10117.974| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.47 r_work: 0.3400 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6625 Z= 0.163 Angle : 0.590 9.615 9003 Z= 0.291 Chirality : 0.042 0.230 941 Planarity : 0.004 0.057 1169 Dihedral : 4.564 55.344 885 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 18.13 % 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: 0.61 (0.30), residues: 788 helix: 2.04 (0.28), residues: 367 sheet: 0.56 (0.83), residues: 49 loop : -1.38 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.021 0.001 PHE A 142 TYR 0.017 0.001 TYR A 385 ARG 0.010 0.001 ARG A 160 *********************** 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: 14 poor density : 162 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8141 (m-40) cc_final: 0.7834 (m-40) REVERT: A 75 GLU cc_start: 0.7792 (tp30) cc_final: 0.7372 (tp30) REVERT: A 77 SER cc_start: 0.8405 (t) cc_final: 0.8141 (m) REVERT: A 87 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7659 (tp30) REVERT: A 126 ILE cc_start: 0.8976 (tp) cc_final: 0.8591 (tt) REVERT: A 165 TRP cc_start: 0.7713 (t60) cc_final: 0.7433 (t60) REVERT: A 181 GLU cc_start: 0.7999 (tt0) cc_final: 0.7722 (mm-30) REVERT: A 206 ASP cc_start: 0.8190 (t0) cc_final: 0.7845 (t0) REVERT: A 213 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 225 ASP cc_start: 0.7203 (m-30) cc_final: 0.6889 (m-30) REVERT: A 250 GLU cc_start: 0.8043 (tp30) cc_final: 0.7659 (tm-30) REVERT: A 297 MET cc_start: 0.8026 (mtt) cc_final: 0.7799 (mtm) REVERT: A 313 LYS cc_start: 0.7987 (tttm) cc_final: 0.7583 (ttmm) REVERT: A 341 LYS cc_start: 0.7948 (mttp) cc_final: 0.7693 (mttm) REVERT: A 347 THR cc_start: 0.8384 (m) cc_final: 0.7977 (p) REVERT: A 358 ILE cc_start: 0.8676 (mt) cc_final: 0.8313 (tt) REVERT: A 482 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7792 (ttm-80) REVERT: A 509 ASP cc_start: 0.8563 (t0) cc_final: 0.8304 (t70) REVERT: A 557 MET cc_start: 0.8303 (tmm) cc_final: 0.7852 (ttp) REVERT: A 563 SER cc_start: 0.8737 (t) cc_final: 0.8210 (p) REVERT: B 501 TYR cc_start: 0.8126 (m-10) cc_final: 0.7786 (m-80) outliers start: 14 outliers final: 10 residues processed: 168 average time/residue: 0.1898 time to fit residues: 42.0821 Evaluate side-chains 168 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU 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 A residue 574 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 75 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 overall best weight: 0.1328 ------------------------------------------------------------------------------- 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 360 ASN B 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117359 restraints weight = 10220.378| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.37 r_work: 0.3405 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3576 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= 0.170 Angle : 0.597 9.614 9003 Z= 0.296 Chirality : 0.042 0.230 941 Planarity : 0.004 0.039 1169 Dihedral : 4.540 55.357 885 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.73 % Allowed : 18.85 % Favored : 79.42 % 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: 0.60 (0.31), residues: 788 helix: 2.06 (0.28), residues: 367 sheet: 0.28 (0.82), residues: 51 loop : -1.38 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE B 456 TYR 0.017 0.001 TYR A 385 ARG 0.008 0.001 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 172 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8245 (m-40) cc_final: 0.7944 (m-40) REVERT: A 75 GLU cc_start: 0.8084 (tp30) cc_final: 0.7634 (tp30) REVERT: A 77 SER cc_start: 0.8516 (t) cc_final: 0.8246 (m) REVERT: A 87 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7813 (mp0) REVERT: A 126 ILE cc_start: 0.9040 (tp) cc_final: 0.8666 (tt) REVERT: A 155 SER cc_start: 0.8575 (t) cc_final: 0.8127 (t) REVERT: A 160 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7225 (ttt-90) REVERT: A 165 TRP cc_start: 0.7666 (t60) cc_final: 0.7438 (t60) REVERT: A 181 GLU cc_start: 0.8208 (tt0) cc_final: 0.7869 (mm-30) REVERT: A 206 ASP cc_start: 0.8385 (t0) cc_final: 0.8023 (t0) REVERT: A 213 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 225 ASP cc_start: 0.7460 (m-30) cc_final: 0.7141 (m-30) REVERT: A 250 GLU cc_start: 0.8261 (tp30) cc_final: 0.7815 (tm-30) REVERT: A 297 MET cc_start: 0.8177 (mtt) cc_final: 0.7941 (mtm) REVERT: A 313 LYS cc_start: 0.8064 (tttm) cc_final: 0.7657 (ttmm) REVERT: A 341 LYS cc_start: 0.8048 (mttp) cc_final: 0.7793 (mttm) REVERT: A 347 THR cc_start: 0.8474 (m) cc_final: 0.8066 (p) REVERT: A 358 ILE cc_start: 0.8744 (mt) cc_final: 0.8397 (tt) REVERT: A 482 ARG cc_start: 0.8229 (ttm170) cc_final: 0.8026 (ttm-80) REVERT: A 509 ASP cc_start: 0.8664 (t0) cc_final: 0.8422 (t70) REVERT: A 557 MET cc_start: 0.8451 (tmm) cc_final: 0.7984 (ttp) REVERT: A 563 SER cc_start: 0.8785 (t) cc_final: 0.8261 (p) REVERT: B 501 TYR cc_start: 0.8232 (m-10) cc_final: 0.7877 (m-80) outliers start: 12 outliers final: 9 residues processed: 164 average time/residue: 0.2250 time to fit residues: 49.1394 Evaluate side-chains 167 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 574 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 0.0070 chunk 47 optimal weight: 0.0060 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 0.0050 chunk 8 optimal weight: 0.6980 overall best weight: 0.1028 ------------------------------------------------------------------------------- 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 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114252 restraints weight = 10347.007| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.45 r_work: 0.3397 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 6625 Z= 0.275 Angle : 1.248 59.194 9003 Z= 0.756 Chirality : 0.049 0.773 941 Planarity : 0.006 0.109 1169 Dihedral : 4.549 55.358 885 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.29 % Allowed : 19.14 % Favored : 79.57 % Cbeta Deviations : 0.27 % 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: 0.58 (0.30), residues: 788 helix: 2.04 (0.28), residues: 368 sheet: 0.23 (0.81), residues: 51 loop : -1.40 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE B 456 TYR 0.017 0.001 TYR A 385 ARG 0.007 0.001 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4583.39 seconds wall clock time: 82 minutes 5.06 seconds (4925.06 seconds total)