Starting phenix.real_space_refine on Fri Apr 5 13:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6a_41067/04_2024/8t6a_41067_updated.pdb" } resolution = 3.17 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1963 2.51 5 N 455 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2947 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2903 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.71 Number of scatterers: 2947 At special positions: 0 Unit cell: (75.933, 65.549, 68.794, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 501 8.00 N 455 7.00 C 1963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 539.1 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 4.216A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 127 through 156 removed outlier: 4.443A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.598A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 Processing helix chain 'A' and resid 182 through 210 removed outlier: 3.649A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 245 removed outlier: 3.827A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.467A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 292 through 322 removed outlier: 4.281A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 4.246A pdb=" N MET A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR A 322 " --> pdb=" O TRP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Proline residue: A 336 - end of helix removed outlier: 3.550A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.775A pdb=" N ILE A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 4.516A pdb=" N MET A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.838A pdb=" N ARG A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 446 Proline residue: A 437 - end of helix removed outlier: 3.843A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 removed outlier: 3.710A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 4.590A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 576 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: 0.81 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 446 1.32 - 1.44: 784 1.44 - 1.56: 1743 1.56 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 3021 Sorted by residual: bond pdb=" C12 YHR A 601 " pdb=" C13 YHR A 601 " ideal model delta sigma weight residual 1.579 1.454 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C10 YHR A 601 " pdb=" C11 YHR A 601 " ideal model delta sigma weight residual 1.572 1.499 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C17 YHR A 601 " pdb=" O19 YHR A 601 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C11 YHR A 601 " pdb=" C23 YHR A 601 " ideal model delta sigma weight residual 1.373 1.437 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C31 YHR A 601 " pdb=" O30 YHR A 601 " ideal model delta sigma weight residual 1.400 1.345 0.055 2.00e-02 2.50e+03 7.65e+00 ... (remaining 3016 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.10: 121 107.10 - 114.03: 1745 114.03 - 120.96: 1564 120.96 - 127.88: 651 127.88 - 134.81: 31 Bond angle restraints: 4112 Sorted by residual: angle pdb=" C25 YHR A 601 " pdb=" C26 YHR A 601 " pdb=" O28 YHR A 601 " ideal model delta sigma weight residual 137.71 123.76 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C27 YHR A 601 " pdb=" C26 YHR A 601 " pdb=" O28 YHR A 601 " ideal model delta sigma weight residual 101.89 114.98 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C9 YHR A 601 " ideal model delta sigma weight residual 99.45 110.81 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C13 YHR A 601 " pdb=" C12 YHR A 601 " pdb=" N21 YHR A 601 " ideal model delta sigma weight residual 132.92 123.79 9.13 3.00e+00 1.11e-01 9.25e+00 angle pdb=" C ILE A 375 " pdb=" CA ILE A 375 " pdb=" CB ILE A 375 " ideal model delta sigma weight residual 114.00 110.04 3.96 1.31e+00 5.83e-01 9.12e+00 ... (remaining 4107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 1684 17.67 - 35.34: 62 35.34 - 53.01: 16 53.01 - 70.68: 3 70.68 - 88.35: 1 Dihedral angle restraints: 1766 sinusoidal: 671 harmonic: 1095 Sorted by residual: dihedral pdb=" CA LEU A 412 " pdb=" C LEU A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL A 269 " pdb=" C VAL A 269 " pdb=" N LEU A 270 " pdb=" CA LEU A 270 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB MET A 204 " pdb=" CG MET A 204 " pdb=" SD MET A 204 " pdb=" CE MET A 204 " ideal model delta sinusoidal sigma weight residual 180.00 121.62 58.38 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 399 0.055 - 0.109: 78 0.109 - 0.164: 8 0.164 - 0.218: 1 0.218 - 0.273: 3 Chirality restraints: 489 Sorted by residual: chirality pdb=" C16 YHR A 601 " pdb=" C15 YHR A 601 " pdb=" C17 YHR A 601 " pdb=" C3 YHR A 601 " both_signs ideal model delta sigma weight residual False 2.75 2.48 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C13 YHR A 601 " pdb=" C12 YHR A 601 " pdb=" C14 YHR A 601 " pdb=" N8 YHR A 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.31 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C6 YHR A 601 " pdb=" C15 YHR A 601 " pdb=" C5 YHR A 601 " pdb=" C7 YHR A 601 " both_signs ideal model delta sigma weight residual False 2.70 2.46 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 486 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 YHR A 601 " 0.044 2.00e-02 2.50e+03 2.11e-02 1.12e+01 pdb=" C33 YHR A 601 " -0.018 2.00e-02 2.50e+03 pdb=" C34 YHR A 601 " -0.024 2.00e-02 2.50e+03 pdb=" C35 YHR A 601 " -0.017 2.00e-02 2.50e+03 pdb=" C36 YHR A 601 " -0.011 2.00e-02 2.50e+03 pdb=" C37 YHR A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C38 YHR A 601 " -0.014 2.00e-02 2.50e+03 pdb=" O39 YHR A 601 " 0.007 2.00e-02 2.50e+03 pdb=" O41 YHR A 601 " 0.026 2.00e-02 2.50e+03 pdb=" O43 YHR A 601 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 YHR A 601 " -0.018 2.00e-02 2.50e+03 1.29e-02 4.96e+00 pdb=" C11 YHR A 601 " 0.011 2.00e-02 2.50e+03 pdb=" C12 YHR A 601 " 0.004 2.00e-02 2.50e+03 pdb=" C13 YHR A 601 " -0.020 2.00e-02 2.50e+03 pdb=" C22 YHR A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C23 YHR A 601 " 0.019 2.00e-02 2.50e+03 pdb=" C24 YHR A 601 " 0.009 2.00e-02 2.50e+03 pdb=" C25 YHR A 601 " -0.005 2.00e-02 2.50e+03 pdb=" C26 YHR A 601 " -0.008 2.00e-02 2.50e+03 pdb=" C27 YHR A 601 " 0.002 2.00e-02 2.50e+03 pdb=" N21 YHR A 601 " 0.007 2.00e-02 2.50e+03 pdb=" O28 YHR A 601 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 236 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.021 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 620 2.78 - 3.31: 3021 3.31 - 3.84: 4981 3.84 - 4.37: 5591 4.37 - 4.90: 10184 Nonbonded interactions: 24397 Sorted by model distance: nonbonded pdb=" OG SER A 200 " pdb=" OH TYR A 422 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 371 " pdb=" O PRO A 387 " model vdw 2.283 2.440 nonbonded pdb=" O LYS A 327 " pdb=" NE2 GLN A 329 " model vdw 2.367 2.520 nonbonded pdb=" O GLU A 215 " pdb=" ND2 ASN A 219 " model vdw 2.375 2.520 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.408 2.520 ... (remaining 24392 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.580 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.005 0.125 3021 Z= 0.368 Angle : 0.816 13.949 4112 Z= 0.359 Chirality : 0.046 0.273 489 Planarity : 0.005 0.037 500 Dihedral : 10.910 88.353 1068 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.28 % Allowed : 2.88 % Favored : 95.83 % 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: 1.58 (0.43), residues: 383 helix: 1.52 (0.30), residues: 308 sheet: None (None), residues: 0 loop : -0.80 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR A 408 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.238 Fit side-chains REVERT: A 471 ARG cc_start: 0.7946 (ttt-90) cc_final: 0.7730 (ttt90) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.1274 time to fit residues: 9.0371 Evaluate side-chains 49 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 329 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3021 Z= 0.251 Angle : 0.606 6.650 4112 Z= 0.316 Chirality : 0.043 0.141 489 Planarity : 0.006 0.035 500 Dihedral : 7.584 82.060 427 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.92 % Allowed : 7.05 % Favored : 91.03 % 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: 1.49 (0.43), residues: 383 helix: 1.51 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.04 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 238 TYR 0.011 0.001 TYR A 49 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.282 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.1260 time to fit residues: 8.3312 Evaluate side-chains 50 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0370 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3021 Z= 0.202 Angle : 0.563 6.587 4112 Z= 0.288 Chirality : 0.041 0.131 489 Planarity : 0.005 0.036 500 Dihedral : 7.465 79.497 427 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.88 % Allowed : 8.01 % Favored : 89.10 % 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: 1.64 (0.43), residues: 383 helix: 1.63 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -0.89 (0.64), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.000 0.000 HIS A 414 PHE 0.013 0.001 PHE A 238 TYR 0.009 0.001 TYR A 49 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.305 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.1271 time to fit residues: 8.9207 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3021 Z= 0.269 Angle : 0.600 6.688 4112 Z= 0.307 Chirality : 0.042 0.139 489 Planarity : 0.006 0.037 500 Dihedral : 7.471 80.296 427 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.88 % Allowed : 10.26 % Favored : 86.86 % 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: 1.43 (0.42), residues: 383 helix: 1.46 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -0.89 (0.64), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.001 HIS A 53 PHE 0.019 0.001 PHE A 238 TYR 0.007 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.236 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1038 time to fit residues: 7.1834 Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0270 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3021 Z= 0.171 Angle : 0.543 6.514 4112 Z= 0.276 Chirality : 0.040 0.124 489 Planarity : 0.005 0.034 500 Dihedral : 7.179 77.787 427 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 11.54 % 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: 1.74 (0.43), residues: 383 helix: 1.67 (0.30), residues: 301 sheet: None (None), residues: 0 loop : -0.69 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 238 TYR 0.005 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.309 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1059 time to fit residues: 7.6859 Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3021 Z= 0.218 Angle : 0.573 6.607 4112 Z= 0.290 Chirality : 0.041 0.134 489 Planarity : 0.005 0.035 500 Dihedral : 7.169 78.117 427 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.56 % Allowed : 11.86 % Favored : 85.58 % 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: 1.78 (0.43), residues: 383 helix: 1.73 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.80 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.006 0.001 TYR A 49 ARG 0.001 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.318 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.1119 time to fit residues: 7.7892 Evaluate side-chains 54 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3021 Z= 0.207 Angle : 0.576 7.411 4112 Z= 0.288 Chirality : 0.041 0.131 489 Planarity : 0.005 0.034 500 Dihedral : 7.025 77.937 427 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.56 % Allowed : 12.50 % Favored : 84.94 % 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: 1.90 (0.43), residues: 383 helix: 1.80 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.66 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.000 HIS A 414 PHE 0.014 0.001 PHE A 238 TYR 0.013 0.001 TYR A 408 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.321 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 52 average time/residue: 0.1096 time to fit residues: 7.5512 Evaluate side-chains 54 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3021 Z= 0.287 Angle : 0.627 7.182 4112 Z= 0.315 Chirality : 0.043 0.144 489 Planarity : 0.006 0.037 500 Dihedral : 7.128 79.465 427 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.56 % Allowed : 12.50 % Favored : 84.94 % 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: 1.61 (0.43), residues: 383 helix: 1.58 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.70 (0.67), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.002 0.000 HIS A 414 PHE 0.020 0.002 PHE A 238 TYR 0.008 0.001 TYR A 49 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.313 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 51 average time/residue: 0.1120 time to fit residues: 7.5066 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3021 Z= 0.237 Angle : 0.594 6.764 4112 Z= 0.298 Chirality : 0.041 0.133 489 Planarity : 0.006 0.038 500 Dihedral : 7.097 78.839 427 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 12.18 % Favored : 85.26 % 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: 1.73 (0.43), residues: 383 helix: 1.66 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.65 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.015 0.001 TYR A 408 ARG 0.002 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.299 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 50 average time/residue: 0.1087 time to fit residues: 7.2056 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3021 Z= 0.239 Angle : 0.596 6.625 4112 Z= 0.298 Chirality : 0.041 0.135 489 Planarity : 0.006 0.038 500 Dihedral : 7.107 78.448 427 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.88 % Allowed : 11.86 % Favored : 85.26 % 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: 1.74 (0.43), residues: 383 helix: 1.67 (0.30), residues: 300 sheet: None (None), residues: 0 loop : -0.65 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 238 TYR 0.007 0.001 TYR A 49 ARG 0.002 0.000 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.299 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.1164 time to fit residues: 7.5396 Evaluate side-chains 51 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 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 = 0.4081 r_free = 0.4081 target = 0.178906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162888 restraints weight = 3013.565| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.91 r_work: 0.3889 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3021 Z= 0.226 Angle : 0.587 6.609 4112 Z= 0.294 Chirality : 0.041 0.132 489 Planarity : 0.006 0.037 500 Dihedral : 7.095 78.055 427 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.21 % Allowed : 11.86 % Favored : 84.94 % 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: 1.79 (0.43), residues: 383 helix: 1.72 (0.30), residues: 299 sheet: None (None), residues: 0 loop : -0.69 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 238 TYR 0.007 0.001 TYR A 49 ARG 0.002 0.000 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.24 seconds wall clock time: 23 minutes 13.07 seconds (1393.07 seconds total)