Starting phenix.real_space_refine on Wed Feb 14 15:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_2024/8gry_34217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_2024/8gry_34217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_2024/8gry_34217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_2024/8gry_34217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gry_34217/02_2024/8gry_34217.pdb" } 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 Residue "A GLU 305": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.97, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.59 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: 1.84 Time building geometry restraints manager: 2.62 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: 98.60 - 105.71: 151 105.71 - 112.82: 3334 112.82 - 119.93: 2356 119.93 - 127.04: 3062 127.04 - 134.15: 100 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 2.520 nonbonded pdb=" OG SER A 607 " pdb=" OD2 ASP A 609 " model vdw 2.234 2.440 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.278 2.440 nonbonded pdb=" NE1 TRP A 478 " pdb=" OD2 ASP A 499 " model vdw 2.286 2.520 ... (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 ========== 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: 8.920 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: 0.000 Extract box with map and model: 27.200 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.120 Find NCS groups from input model: 0.170 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.890 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 0.707 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: 0.2202 time to fit residues: 58.4687 Evaluate side-chains 181 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 0.4980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 45 optimal weight: 0.0070 chunk 70 optimal weight: 0.1980 overall best weight: 0.1976 ------------------------------------------------------------------------------- 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 A 368 ASN B 422 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1884 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= 0.179 Angle : 0.558 9.736 9003 Z= 0.279 Chirality : 0.042 0.218 941 Planarity : 0.004 0.053 1169 Dihedral : 5.304 56.700 885 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.87 % Allowed : 8.35 % 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: 0.77 (0.31), residues: 788 helix: 2.04 (0.28), residues: 374 sheet: 0.63 (0.86), residues: 49 loop : -1.20 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.012 0.001 PHE A 592 TYR 0.019 0.001 TYR A 385 ARG 0.004 0.000 ARG A 340 *********************** 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 196 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7317 (tp30) cc_final: 0.6857 (tp30) REVERT: A 77 SER cc_start: 0.8113 (t) cc_final: 0.7802 (m) REVERT: A 126 ILE cc_start: 0.8875 (tp) cc_final: 0.8513 (tt) REVERT: A 181 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: A 182 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 186 LEU cc_start: 0.7442 (mm) cc_final: 0.6901 (mm) REVERT: A 197 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6299 (tm-30) REVERT: A 206 ASP cc_start: 0.7736 (t0) cc_final: 0.7481 (t0) REVERT: A 213 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 225 ASP cc_start: 0.6728 (m-30) cc_final: 0.6428 (m-30) REVERT: A 250 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7446 (tp30) REVERT: A 313 LYS cc_start: 0.7813 (tttt) cc_final: 0.7498 (ttmm) REVERT: A 341 LYS cc_start: 0.7709 (mttp) cc_final: 0.7431 (mttp) REVERT: A 347 THR cc_start: 0.7943 (m) cc_final: 0.7714 (p) REVERT: A 375 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 458 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7355 (tptm) REVERT: A 469 PRO cc_start: 0.8745 (Cg_exo) cc_final: 0.8521 (Cg_endo) REVERT: A 472 GLN cc_start: 0.7855 (mp10) cc_final: 0.7538 (mp10) REVERT: A 475 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7797 (ttpt) REVERT: A 476 LYS cc_start: 0.7851 (tppt) cc_final: 0.7619 (tppp) REVERT: A 482 ARG cc_start: 0.7251 (ttm170) cc_final: 0.6974 (ttm-80) REVERT: A 517 THR cc_start: 0.6983 (p) cc_final: 0.6589 (p) REVERT: A 557 MET cc_start: 0.7834 (tmm) cc_final: 0.7577 (ttp) REVERT: A 574 VAL cc_start: 0.8397 (m) cc_final: 0.8194 (p) REVERT: B 336 CYS cc_start: 0.3991 (m) cc_final: 0.3310 (m) REVERT: B 357 ARG cc_start: 0.6573 (ptm-80) cc_final: 0.6227 (ptm-80) REVERT: B 469 SER cc_start: 0.8276 (t) cc_final: 0.8039 (t) outliers start: 13 outliers final: 9 residues processed: 188 average time/residue: 0.2144 time to fit residues: 51.5930 Evaluate side-chains 186 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 334 THR 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: 0.7980 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 0.2980 chunk 53 optimal weight: 0.0040 overall best weight: 0.2992 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2612 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= 0.231 Angle : 0.573 9.934 9003 Z= 0.291 Chirality : 0.043 0.273 941 Planarity : 0.004 0.049 1169 Dihedral : 5.007 54.692 885 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.01 % Allowed : 11.94 % Favored : 86.04 % 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: 0.68 (0.31), residues: 788 helix: 1.94 (0.28), residues: 374 sheet: 0.50 (0.85), residues: 51 loop : -1.21 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.002 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG B 466 *********************** 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 195 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7521 (ttpp) cc_final: 0.7303 (tttp) REVERT: A 75 GLU cc_start: 0.7306 (tp30) cc_final: 0.6832 (tp30) REVERT: A 126 ILE cc_start: 0.8984 (tp) cc_final: 0.8584 (tt) REVERT: A 181 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 206 ASP cc_start: 0.7719 (t0) cc_final: 0.7435 (t0) REVERT: A 213 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7036 (mm-30) REVERT: A 225 ASP cc_start: 0.6786 (m-30) cc_final: 0.6437 (m-30) REVERT: A 250 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7533 (tp30) REVERT: A 458 LYS cc_start: 0.7553 (tttt) cc_final: 0.7348 (tttt) REVERT: A 462 MET cc_start: 0.7700 (mtp) cc_final: 0.7447 (mtt) REVERT: A 472 GLN cc_start: 0.7841 (mp10) cc_final: 0.7571 (mp10) REVERT: A 475 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7844 (ttpt) REVERT: A 482 ARG cc_start: 0.7362 (ttm170) cc_final: 0.7061 (ttm-80) REVERT: A 543 ASP cc_start: 0.6810 (m-30) cc_final: 0.6567 (m-30) REVERT: A 557 MET cc_start: 0.7894 (tmm) cc_final: 0.7578 (ttp) REVERT: A 562 ASN cc_start: 0.7634 (t0) cc_final: 0.7353 (t0) REVERT: B 357 ARG cc_start: 0.6599 (ptm-80) cc_final: 0.6213 (ptm-80) REVERT: B 393 THR cc_start: 0.6920 (m) cc_final: 0.6576 (p) outliers start: 14 outliers final: 10 residues processed: 185 average time/residue: 0.2224 time to fit residues: 52.1664 Evaluate side-chains 186 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 335 LEU 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: 0.0980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 0.0980 chunk 75 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 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 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2802 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= 0.173 Angle : 0.549 9.711 9003 Z= 0.275 Chirality : 0.041 0.252 941 Planarity : 0.004 0.044 1169 Dihedral : 4.616 55.583 885 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.16 % Allowed : 14.10 % Favored : 83.74 % 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: 0.78 (0.31), residues: 788 helix: 2.07 (0.28), residues: 364 sheet: 1.75 (0.93), residues: 41 loop : -1.25 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.017 0.001 TYR A 385 ARG 0.003 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 183 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7310 (tp30) cc_final: 0.7007 (tp30) REVERT: A 77 SER cc_start: 0.8089 (t) cc_final: 0.7780 (m) REVERT: A 113 ASN cc_start: 0.8610 (t0) cc_final: 0.8407 (t0) REVERT: A 126 ILE cc_start: 0.8988 (tp) cc_final: 0.8578 (tt) REVERT: A 152 MET cc_start: 0.7089 (mmm) cc_final: 0.6853 (mmm) REVERT: A 182 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7494 (pp20) REVERT: A 206 ASP cc_start: 0.7757 (t0) cc_final: 0.7428 (t0) REVERT: A 213 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 225 ASP cc_start: 0.6712 (m-30) cc_final: 0.6349 (m-30) REVERT: A 250 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7441 (tp30) REVERT: A 313 LYS cc_start: 0.7890 (tttt) cc_final: 0.7490 (ttmm) REVERT: A 458 LYS cc_start: 0.7562 (tttt) cc_final: 0.7289 (tptm) REVERT: A 472 GLN cc_start: 0.7801 (mp10) cc_final: 0.7476 (mp10) REVERT: A 475 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7835 (ttpt) REVERT: A 476 LYS cc_start: 0.7829 (tppt) cc_final: 0.7615 (tppp) REVERT: A 482 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6953 (ttm-80) REVERT: A 517 THR cc_start: 0.6946 (p) cc_final: 0.6668 (p) REVERT: A 557 MET cc_start: 0.7891 (tmm) cc_final: 0.7531 (ttp) REVERT: B 357 ARG cc_start: 0.6577 (ptm-80) cc_final: 0.6196 (ptm-80) outliers start: 15 outliers final: 12 residues processed: 174 average time/residue: 0.2015 time to fit residues: 45.3247 Evaluate side-chains 185 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 216 ASN Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 335 LEU 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: 0.8980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 67 optimal weight: 0.0040 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 overall best weight: 0.1370 ------------------------------------------------------------------------------- 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: 0.7374 moved from start: 0.2922 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= 0.155 Angle : 0.534 9.696 9003 Z= 0.266 Chirality : 0.040 0.248 941 Planarity : 0.004 0.041 1169 Dihedral : 4.392 55.355 885 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.30 % Allowed : 15.40 % Favored : 82.30 % 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: 0.83 (0.31), residues: 788 helix: 2.13 (0.28), residues: 364 sheet: 1.63 (0.92), residues: 41 loop : -1.23 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 369 TYR 0.018 0.001 TYR A 385 ARG 0.005 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 179 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7322 (tp30) cc_final: 0.7009 (tp30) REVERT: A 77 SER cc_start: 0.8077 (t) cc_final: 0.7777 (m) REVERT: A 113 ASN cc_start: 0.8605 (t0) cc_final: 0.8393 (t0) REVERT: A 126 ILE cc_start: 0.8977 (tp) cc_final: 0.8572 (tt) REVERT: A 152 MET cc_start: 0.6891 (mmm) cc_final: 0.6395 (mmm) REVERT: A 206 ASP cc_start: 0.7763 (t0) cc_final: 0.7399 (t0) REVERT: A 213 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 225 ASP cc_start: 0.6720 (m-30) cc_final: 0.6338 (m-30) REVERT: A 313 LYS cc_start: 0.7902 (tttt) cc_final: 0.7495 (ttmm) REVERT: A 458 LYS cc_start: 0.7578 (tttt) cc_final: 0.7330 (tptm) REVERT: A 475 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7838 (ttpt) REVERT: A 482 ARG cc_start: 0.7375 (ttm170) cc_final: 0.7138 (ttm-80) REVERT: A 517 THR cc_start: 0.6895 (p) cc_final: 0.6609 (p) REVERT: A 557 MET cc_start: 0.7852 (tmm) cc_final: 0.7515 (ttp) REVERT: A 562 ASN cc_start: 0.7574 (t0) cc_final: 0.7194 (t0) REVERT: B 357 ARG cc_start: 0.6577 (ptm-80) cc_final: 0.6365 (ptm-80) outliers start: 16 outliers final: 12 residues processed: 171 average time/residue: 0.1874 time to fit residues: 42.1922 Evaluate side-chains 173 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 216 ASN Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 75 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.0010 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 39 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.1704 ------------------------------------------------------------------------------- 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: 0.7386 moved from start: 0.3050 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= 0.168 Angle : 0.560 9.647 9003 Z= 0.277 Chirality : 0.042 0.244 941 Planarity : 0.004 0.041 1169 Dihedral : 4.482 55.585 885 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.01 % Allowed : 16.55 % 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: 0.81 (0.31), residues: 788 helix: 2.12 (0.28), residues: 365 sheet: 1.81 (0.93), residues: 39 loop : -1.26 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.012 0.001 PHE A 504 TYR 0.017 0.001 TYR A 385 ARG 0.004 0.000 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 175 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7294 (ttpp) cc_final: 0.7078 (tttt) REVERT: A 75 GLU cc_start: 0.7318 (tp30) cc_final: 0.7008 (tp30) REVERT: A 77 SER cc_start: 0.8083 (t) cc_final: 0.7788 (m) REVERT: A 98 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7155 (ttpp) REVERT: A 113 ASN cc_start: 0.8598 (t0) cc_final: 0.8397 (t0) REVERT: A 126 ILE cc_start: 0.8973 (tp) cc_final: 0.8572 (tt) REVERT: A 152 MET cc_start: 0.6673 (mmm) cc_final: 0.6388 (mmm) REVERT: A 206 ASP cc_start: 0.7739 (t0) cc_final: 0.7356 (t0) REVERT: A 213 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 225 ASP cc_start: 0.6732 (m-30) cc_final: 0.6334 (m-30) REVERT: A 313 LYS cc_start: 0.7948 (tttt) cc_final: 0.7531 (ttmm) REVERT: A 358 ILE cc_start: 0.8597 (mt) cc_final: 0.8209 (tt) REVERT: A 458 LYS cc_start: 0.7575 (tttt) cc_final: 0.7330 (tptm) REVERT: A 475 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7840 (ttpt) REVERT: A 482 ARG cc_start: 0.7438 (ttm170) cc_final: 0.7217 (ttm-80) REVERT: A 557 MET cc_start: 0.7850 (tmm) cc_final: 0.7506 (ttp) REVERT: A 562 ASN cc_start: 0.7653 (t0) cc_final: 0.7426 (t0) REVERT: B 357 ARG cc_start: 0.6594 (ptm-80) cc_final: 0.6390 (ptm-80) REVERT: B 501 TYR cc_start: 0.7969 (m-10) cc_final: 0.7447 (m-80) outliers start: 14 outliers final: 12 residues processed: 168 average time/residue: 0.1990 time to fit residues: 43.5944 Evaluate side-chains 173 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 376 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 overall best weight: 0.2118 ------------------------------------------------------------------------------- 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: 0.7404 moved from start: 0.3173 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 : 0.558 9.633 9003 Z= 0.279 Chirality : 0.042 0.242 941 Planarity : 0.004 0.041 1169 Dihedral : 4.565 55.550 885 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.01 % Allowed : 16.83 % 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: 0.73 (0.31), residues: 788 helix: 2.10 (0.28), residues: 365 sheet: 1.48 (0.91), residues: 41 loop : -1.34 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 504 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 *********************** 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 176 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7383 (ttpp) cc_final: 0.7173 (tttt) REVERT: A 75 GLU cc_start: 0.7308 (tp30) cc_final: 0.7000 (tp30) REVERT: A 77 SER cc_start: 0.8092 (t) cc_final: 0.7809 (m) REVERT: A 87 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7278 (tp30) REVERT: A 113 ASN cc_start: 0.8610 (t0) cc_final: 0.8389 (t0) REVERT: A 126 ILE cc_start: 0.8971 (tp) cc_final: 0.8572 (tt) REVERT: A 152 MET cc_start: 0.6729 (mmm) cc_final: 0.6317 (mmm) REVERT: A 206 ASP cc_start: 0.7761 (t0) cc_final: 0.7414 (t0) REVERT: A 213 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 225 ASP cc_start: 0.6776 (m-30) cc_final: 0.6365 (m-30) REVERT: A 269 ASP cc_start: 0.7546 (t0) cc_final: 0.7250 (t0) REVERT: A 313 LYS cc_start: 0.7951 (tttt) cc_final: 0.7530 (ttmm) REVERT: A 458 LYS cc_start: 0.7570 (tttt) cc_final: 0.7335 (tptm) REVERT: A 475 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7821 (ttpt) REVERT: A 476 LYS cc_start: 0.7885 (tppt) cc_final: 0.7667 (tppp) REVERT: A 482 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7216 (ttm-80) REVERT: A 517 THR cc_start: 0.6984 (p) cc_final: 0.6699 (p) REVERT: A 557 MET cc_start: 0.7865 (tmm) cc_final: 0.7520 (ttp) REVERT: A 562 ASN cc_start: 0.7720 (t0) cc_final: 0.7498 (t0) REVERT: B 501 TYR cc_start: 0.8013 (m-10) cc_final: 0.7507 (m-80) outliers start: 14 outliers final: 11 residues processed: 168 average time/residue: 0.1856 time to fit residues: 40.8142 Evaluate side-chains 175 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 376 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 0.0980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.0170 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 overall best weight: 0.1054 ------------------------------------------------------------------------------- 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: 0.7357 moved from start: 0.3217 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 : 0.548 9.874 9003 Z= 0.268 Chirality : 0.041 0.233 941 Planarity : 0.004 0.041 1169 Dihedral : 4.406 55.440 885 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.44 % Allowed : 18.13 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.31), residues: 788 helix: 2.20 (0.28), residues: 365 sheet: 1.81 (0.92), residues: 39 loop : -1.31 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 373 PHE 0.013 0.001 PHE A 142 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 *********************** 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 171 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7316 (tp30) cc_final: 0.7012 (tp30) REVERT: A 77 SER cc_start: 0.8080 (t) cc_final: 0.7787 (m) REVERT: A 87 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7265 (tp30) REVERT: A 98 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7156 (ttpp) REVERT: A 113 ASN cc_start: 0.8585 (t0) cc_final: 0.8380 (t0) REVERT: A 126 ILE cc_start: 0.8922 (tp) cc_final: 0.8692 (tp) REVERT: A 152 MET cc_start: 0.6655 (mmm) cc_final: 0.6255 (mmm) REVERT: A 206 ASP cc_start: 0.7808 (t0) cc_final: 0.7501 (t0) REVERT: A 213 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 313 LYS cc_start: 0.7937 (tttt) cc_final: 0.7510 (ttmm) REVERT: A 458 LYS cc_start: 0.7585 (tttt) cc_final: 0.7358 (tptm) REVERT: A 476 LYS cc_start: 0.7834 (tppt) cc_final: 0.7611 (tppp) REVERT: A 482 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7225 (ttm-80) REVERT: A 557 MET cc_start: 0.7825 (tmm) cc_final: 0.7470 (ttp) REVERT: A 562 ASN cc_start: 0.7660 (t0) cc_final: 0.7347 (t0) REVERT: B 501 TYR cc_start: 0.7988 (m-10) cc_final: 0.7434 (m-80) outliers start: 10 outliers final: 8 residues processed: 166 average time/residue: 0.2019 time to fit residues: 44.3710 Evaluate side-chains 164 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 257 SER Chi-restraints excluded: chain A residue 376 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.0020 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3454 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= 0.275 Angle : 0.606 9.660 9003 Z= 0.310 Chirality : 0.044 0.247 941 Planarity : 0.004 0.042 1169 Dihedral : 4.757 55.898 885 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.01 % Allowed : 18.27 % 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: 0.69 (0.31), residues: 788 helix: 2.05 (0.28), residues: 364 sheet: 1.86 (0.92), residues: 39 loop : -1.36 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE A 592 TYR 0.017 0.001 TYR A 385 ARG 0.004 0.000 ARG B 357 *********************** 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 184 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7487 (ttpp) cc_final: 0.7284 (tttt) REVERT: A 61 LYS cc_start: 0.8114 (mttt) cc_final: 0.7774 (mttm) REVERT: A 75 GLU cc_start: 0.7291 (tp30) cc_final: 0.6969 (tp30) REVERT: A 113 ASN cc_start: 0.8640 (t0) cc_final: 0.8409 (t0) REVERT: A 126 ILE cc_start: 0.9000 (tp) cc_final: 0.8593 (tt) REVERT: A 152 MET cc_start: 0.6730 (mmm) cc_final: 0.6248 (mmm) REVERT: A 155 SER cc_start: 0.8746 (t) cc_final: 0.7940 (m) REVERT: A 206 ASP cc_start: 0.7728 (t0) cc_final: 0.7460 (t0) REVERT: A 213 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 225 ASP cc_start: 0.6815 (m-30) cc_final: 0.6397 (m-30) REVERT: A 269 ASP cc_start: 0.7566 (t0) cc_final: 0.7263 (t0) REVERT: A 313 LYS cc_start: 0.7966 (tttt) cc_final: 0.7505 (ttmm) REVERT: A 458 LYS cc_start: 0.7555 (tttt) cc_final: 0.7347 (tptm) REVERT: A 476 LYS cc_start: 0.7941 (tppt) cc_final: 0.7713 (tppp) REVERT: A 482 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7227 (ttm-80) REVERT: A 517 THR cc_start: 0.7074 (p) cc_final: 0.6824 (p) REVERT: A 557 MET cc_start: 0.7894 (tmm) cc_final: 0.7533 (ttp) REVERT: B 501 TYR cc_start: 0.8024 (m-10) cc_final: 0.7609 (m-80) outliers start: 14 outliers final: 13 residues processed: 176 average time/residue: 0.2115 time to fit residues: 48.5114 Evaluate side-chains 181 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6625 Z= 0.290 Angle : 1.242 59.200 9003 Z= 0.754 Chirality : 0.048 0.607 941 Planarity : 0.005 0.059 1169 Dihedral : 4.803 55.903 885 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.01 % Allowed : 18.85 % Favored : 79.14 % Cbeta Deviations : 0.13 % 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 (0.30), residues: 788 helix: 2.02 (0.28), residues: 364 sheet: 1.73 (0.91), residues: 39 loop : -1.40 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE A 592 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 169 ********************** 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 184 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7485 (ttpp) cc_final: 0.7280 (tttt) REVERT: A 61 LYS cc_start: 0.8105 (mttt) cc_final: 0.7770 (mttm) REVERT: A 75 GLU cc_start: 0.7280 (tp30) cc_final: 0.6966 (tp30) REVERT: A 113 ASN cc_start: 0.8641 (t0) cc_final: 0.8405 (t0) REVERT: A 126 ILE cc_start: 0.9003 (tp) cc_final: 0.8590 (tt) REVERT: A 152 MET cc_start: 0.6712 (mmm) cc_final: 0.6235 (mmm) REVERT: A 155 SER cc_start: 0.8745 (t) cc_final: 0.7935 (m) REVERT: A 206 ASP cc_start: 0.7720 (t0) cc_final: 0.7458 (t0) REVERT: A 213 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 225 ASP cc_start: 0.6807 (m-30) cc_final: 0.6381 (m-30) REVERT: A 269 ASP cc_start: 0.7567 (t0) cc_final: 0.7264 (t0) REVERT: A 313 LYS cc_start: 0.7963 (tttt) cc_final: 0.7503 (ttmm) REVERT: A 458 LYS cc_start: 0.7565 (tttt) cc_final: 0.7341 (tptm) REVERT: A 476 LYS cc_start: 0.7939 (tppt) cc_final: 0.7706 (tppp) REVERT: A 482 ARG cc_start: 0.7484 (ttm170) cc_final: 0.7219 (ttm-80) REVERT: A 517 THR cc_start: 0.7064 (p) cc_final: 0.6819 (p) REVERT: A 557 MET cc_start: 0.7892 (tmm) cc_final: 0.7522 (ttp) REVERT: B 501 TYR cc_start: 0.8027 (m-10) cc_final: 0.7551 (m-80) outliers start: 14 outliers final: 12 residues processed: 175 average time/residue: 0.1957 time to fit residues: 44.4567 Evaluate side-chains 181 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 overall best weight: 0.1552 ------------------------------------------------------------------------------- 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 B 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113839 restraints weight = 10019.519| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.26 r_work: 0.3347 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6625 Z= 0.290 Angle : 1.242 59.200 9003 Z= 0.754 Chirality : 0.048 0.607 941 Planarity : 0.005 0.059 1169 Dihedral : 4.803 55.903 885 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.87 % Allowed : 19.28 % Favored : 78.85 % Cbeta Deviations : 0.13 % 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 (0.30), residues: 788 helix: 2.02 (0.28), residues: 364 sheet: 1.73 (0.91), residues: 39 loop : -1.40 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE A 592 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.32 seconds wall clock time: 45 minutes 34.67 seconds (2734.67 seconds total)