Starting phenix.real_space_refine on Thu Jul 18 18:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6b_41068/07_2024/8t6b_41068.cif" } resolution = 3.72 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= 0.017 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 1940 2.51 5 N 455 2.21 5 O 493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2916 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.96 Number of scatterers: 2916 At special positions: 0 Unit cell: (76.582, 66.198, 72.688, 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 493 8.00 N 455 7.00 C 1940 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: 0.99 Conformation dependent library (CDL) restraints added in 648.6 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... Secondary structure from input PDB file: 21 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.619A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.696A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.654A 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 removed outlier: 3.508A pdb=" N LYS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.388A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.560A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 212 removed outlier: 4.014A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 5.039A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.679A pdb=" N MET A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.094A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 4.658A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.866A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.619A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.918A pdb=" N LEU A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.638A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.679A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 412 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 447 removed outlier: 3.881A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.016A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.694A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.864A pdb=" N SER A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 606 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: 0.73 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 873 1.35 - 1.46: 702 1.46 - 1.58: 1363 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2986 Sorted by residual: bond pdb=" CG LEU A 409 " pdb=" CD1 LEU A 409 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" C ALA A 464 " pdb=" N PRO A 465 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.19e-02 7.06e+03 2.74e+00 bond pdb=" CA VAL A 41 " pdb=" CB VAL A 41 " ideal model delta sigma weight residual 1.534 1.544 -0.010 6.80e-03 2.16e+04 2.03e+00 bond pdb=" CA VAL A 41 " pdb=" C VAL A 41 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.58e+00 bond pdb=" CA SER A 400 " pdb=" C SER A 400 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.41e-02 5.03e+03 1.41e+00 ... (remaining 2981 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.15: 123 107.15 - 113.92: 1687 113.92 - 120.69: 1335 120.69 - 127.46: 881 127.46 - 134.22: 33 Bond angle restraints: 4059 Sorted by residual: angle pdb=" C GLY A 247 " pdb=" N LYS A 248 " pdb=" CA LYS A 248 " ideal model delta sigma weight residual 120.28 124.94 -4.66 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.41 -6.60 2.21e+00 2.05e-01 8.93e+00 angle pdb=" C VAL A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta sigma weight residual 120.24 122.06 -1.82 6.30e-01 2.52e+00 8.34e+00 angle pdb=" C PHE A 463 " pdb=" N ALA A 464 " pdb=" CA ALA A 464 " ideal model delta sigma weight residual 120.58 124.34 -3.76 1.32e+00 5.74e-01 8.10e+00 angle pdb=" N ILE A 447 " pdb=" CA ILE A 447 " pdb=" C ILE A 447 " ideal model delta sigma weight residual 113.71 111.17 2.54 9.50e-01 1.11e+00 7.14e+00 ... (remaining 4054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1531 15.53 - 31.06: 160 31.06 - 46.59: 52 46.59 - 62.12: 6 62.12 - 77.65: 3 Dihedral angle restraints: 1752 sinusoidal: 657 harmonic: 1095 Sorted by residual: dihedral pdb=" CA PHE A 184 " pdb=" C PHE A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASN A 34 " pdb=" C ASN A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA THR A 38 " pdb=" C THR A 38 " pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.057: 127 0.057 - 0.085: 51 0.085 - 0.113: 30 0.113 - 0.142: 3 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA VAL A 417 " pdb=" N VAL A 417 " pdb=" C VAL A 417 " pdb=" CB VAL A 417 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO A 161 " pdb=" N PRO A 161 " pdb=" C PRO A 161 " pdb=" CB PRO A 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL A 415 " pdb=" N VAL A 415 " pdb=" C VAL A 415 " pdb=" CB VAL A 415 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 480 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 244 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CD GLU A 244 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 244 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 244 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 312 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 313 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.023 5.00e-02 4.00e+02 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 576 2.77 - 3.30: 2987 3.30 - 3.83: 4767 3.83 - 4.37: 5321 4.37 - 4.90: 9352 Nonbonded interactions: 23003 Sorted by model distance: nonbonded pdb=" OH TYR A 293 " pdb=" O PHE A 469 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR A 212 " pdb=" N ASP A 213 " model vdw 2.434 2.520 nonbonded pdb=" O TYR A 211 " pdb=" OG1 THR A 212 " model vdw 2.475 2.440 nonbonded pdb=" OH TYR A 158 " pdb=" OE2 GLU A 278 " model vdw 2.497 2.440 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.499 2.520 ... (remaining 22998 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.004 0.058 2986 Z= 0.239 Angle : 0.785 8.888 4059 Z= 0.419 Chirality : 0.042 0.142 483 Planarity : 0.006 0.045 497 Dihedral : 14.454 77.650 1054 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.42), residues: 383 helix: -0.53 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.62 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 27 TYR 0.008 0.001 TYR A 341 ARG 0.004 0.001 ARG A 19 *********************** 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 50 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1171 time to fit residues: 7.5540 Evaluate side-chains 49 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3842 ------------------------------------------------------------------------------- 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: 0.6521 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2986 Z= 0.201 Angle : 0.662 6.645 4059 Z= 0.326 Chirality : 0.042 0.149 483 Planarity : 0.006 0.042 497 Dihedral : 6.662 62.350 409 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.21 % Allowed : 17.31 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.43), residues: 383 helix: -0.02 (0.30), residues: 307 sheet: None (None), residues: 0 loop : -1.37 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 468 TYR 0.013 0.001 TYR A 243 ARG 0.003 0.001 ARG A 19 *********************** 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 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.276 Fit side-chains REVERT: A 365 MET cc_start: 0.5481 (mmm) cc_final: 0.5149 (mmm) outliers start: 10 outliers final: 5 residues processed: 55 average time/residue: 0.1092 time to fit residues: 7.9512 Evaluate side-chains 50 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.6641 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2986 Z= 0.269 Angle : 0.700 6.955 4059 Z= 0.345 Chirality : 0.044 0.155 483 Planarity : 0.006 0.042 497 Dihedral : 6.049 42.664 409 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.45 % Allowed : 16.35 % Favored : 78.21 % 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: -0.54 (0.44), residues: 383 helix: 0.00 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.33 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.002 0.001 HIS A 414 PHE 0.013 0.001 PHE A 27 TYR 0.010 0.001 TYR A 243 ARG 0.003 0.001 ARG A 274 *********************** 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 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.302 Fit side-chains REVERT: A 365 MET cc_start: 0.5906 (mmm) cc_final: 0.5393 (mmm) REVERT: A 389 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5167 (t80) outliers start: 17 outliers final: 10 residues processed: 66 average time/residue: 0.1091 time to fit residues: 9.2588 Evaluate side-chains 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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: 0.6602 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2986 Z= 0.221 Angle : 0.701 13.647 4059 Z= 0.333 Chirality : 0.042 0.158 483 Planarity : 0.006 0.040 497 Dihedral : 5.632 32.697 409 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 7.05 % Allowed : 16.03 % Favored : 76.92 % 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 (0.44), residues: 383 helix: 0.14 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.57 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 468 TYR 0.015 0.001 TYR A 243 ARG 0.006 0.001 ARG A 326 *********************** 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 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.244 Fit side-chains REVERT: A 148 PHE cc_start: 0.6281 (m-10) cc_final: 0.4788 (t80) REVERT: A 365 MET cc_start: 0.5788 (mmm) cc_final: 0.5215 (mmm) REVERT: A 389 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5147 (t80) outliers start: 22 outliers final: 13 residues processed: 59 average time/residue: 0.1040 time to fit residues: 7.9321 Evaluate side-chains 58 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.6703 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2986 Z= 0.296 Angle : 0.749 10.809 4059 Z= 0.359 Chirality : 0.045 0.170 483 Planarity : 0.006 0.039 497 Dihedral : 5.894 48.580 409 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 8.33 % Allowed : 15.06 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.43), residues: 383 helix: -0.05 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -1.39 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 468 TYR 0.011 0.001 TYR A 243 ARG 0.004 0.001 ARG A 326 *********************** 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 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 51 time to evaluate : 0.286 Fit side-chains REVERT: A 148 PHE cc_start: 0.6367 (m-10) cc_final: 0.4722 (t80) REVERT: A 365 MET cc_start: 0.5972 (mmm) cc_final: 0.5389 (mmm) REVERT: A 389 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5166 (t80) outliers start: 26 outliers final: 15 residues processed: 70 average time/residue: 0.1009 time to fit residues: 9.2582 Evaluate side-chains 63 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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: 0.6568 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2986 Z= 0.185 Angle : 0.677 9.197 4059 Z= 0.318 Chirality : 0.041 0.154 483 Planarity : 0.006 0.052 497 Dihedral : 5.491 46.262 409 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.77 % Allowed : 18.59 % Favored : 75.64 % 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: -0.34 (0.44), residues: 383 helix: 0.26 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -1.73 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.008 0.001 PHE A 27 TYR 0.006 0.001 TYR A 243 ARG 0.003 0.000 ARG A 326 *********************** 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 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.294 Fit side-chains REVERT: A 148 PHE cc_start: 0.6307 (m-10) cc_final: 0.4885 (t80) REVERT: A 169 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5051 (mtt) REVERT: A 192 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 359 LEU cc_start: 0.6844 (mt) cc_final: 0.6515 (mp) REVERT: A 365 MET cc_start: 0.5878 (mmm) cc_final: 0.5246 (mmm) REVERT: A 389 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5087 (t80) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.1141 time to fit residues: 9.0379 Evaluate side-chains 64 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6635 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2986 Z= 0.236 Angle : 0.713 8.053 4059 Z= 0.335 Chirality : 0.043 0.163 483 Planarity : 0.006 0.045 497 Dihedral : 5.630 51.306 409 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.70 % Favored : 95.04 % Rotamer: Outliers : 6.41 % Allowed : 18.91 % Favored : 74.68 % 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: -0.32 (0.44), residues: 383 helix: 0.20 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -1.47 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.001 HIS A 353 PHE 0.011 0.001 PHE A 468 TYR 0.008 0.001 TYR A 211 ARG 0.003 0.001 ARG A 357 *********************** 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 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.301 Fit side-chains REVERT: A 148 PHE cc_start: 0.6320 (m-10) cc_final: 0.4848 (t80) REVERT: A 169 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5082 (mtt) REVERT: A 192 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 365 MET cc_start: 0.5941 (mmm) cc_final: 0.5323 (mmm) REVERT: A 389 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5117 (t80) outliers start: 20 outliers final: 12 residues processed: 61 average time/residue: 0.0986 time to fit residues: 7.9610 Evaluate side-chains 62 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.6578 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2986 Z= 0.197 Angle : 0.699 8.517 4059 Z= 0.324 Chirality : 0.042 0.156 483 Planarity : 0.006 0.041 497 Dihedral : 5.517 51.504 409 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.44 % Favored : 95.30 % Rotamer: Outliers : 6.09 % Allowed : 19.55 % Favored : 74.36 % 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: -0.16 (0.44), residues: 383 helix: 0.37 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.64 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 166 TYR 0.005 0.001 TYR A 211 ARG 0.002 0.000 ARG A 326 *********************** 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 70 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.298 Fit side-chains REVERT: A 148 PHE cc_start: 0.6299 (m-10) cc_final: 0.4888 (t80) REVERT: A 169 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.5005 (mtt) REVERT: A 192 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 359 LEU cc_start: 0.6863 (mt) cc_final: 0.6463 (mp) REVERT: A 389 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5157 (t80) outliers start: 19 outliers final: 14 residues processed: 62 average time/residue: 0.1040 time to fit residues: 8.4188 Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 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: 0.6611 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2986 Z= 0.224 Angle : 0.715 7.314 4059 Z= 0.335 Chirality : 0.043 0.194 483 Planarity : 0.006 0.038 497 Dihedral : 5.634 54.473 409 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.44 % Favored : 95.30 % Rotamer: Outliers : 6.09 % Allowed : 20.19 % Favored : 73.72 % 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: -0.21 (0.44), residues: 383 helix: 0.28 (0.30), residues: 306 sheet: None (None), residues: 0 loop : -1.45 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.010 0.001 PHE A 27 TYR 0.008 0.001 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** 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 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.270 Fit side-chains REVERT: A 148 PHE cc_start: 0.6343 (m-10) cc_final: 0.4905 (t80) REVERT: A 169 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5088 (mtt) REVERT: A 192 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 389 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.5186 (t80) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.0989 time to fit residues: 8.1214 Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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: 0.6597 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2986 Z= 0.219 Angle : 0.719 7.786 4059 Z= 0.335 Chirality : 0.043 0.181 483 Planarity : 0.006 0.049 497 Dihedral : 5.669 56.722 409 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.44 % Favored : 95.30 % Rotamer: Outliers : 5.77 % Allowed : 20.19 % Favored : 74.04 % 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: -0.15 (0.44), residues: 383 helix: 0.36 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -1.56 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 27 TYR 0.007 0.001 TYR A 211 ARG 0.002 0.000 ARG A 326 ********************** 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 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.297 Fit side-chains REVERT: A 148 PHE cc_start: 0.6356 (m-10) cc_final: 0.4938 (t80) REVERT: A 169 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.5102 (mtt) REVERT: A 192 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 389 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5177 (t80) outliers start: 18 outliers final: 14 residues processed: 63 average time/residue: 0.1149 time to fit residues: 9.2624 Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.183461 restraints weight = 3611.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.187542 restraints weight = 2286.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.190156 restraints weight = 1608.191| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2986 Z= 0.204 Angle : 0.705 7.474 4059 Z= 0.328 Chirality : 0.042 0.168 483 Planarity : 0.006 0.049 497 Dihedral : 5.640 58.104 409 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer: Outliers : 5.77 % Allowed : 20.19 % Favored : 74.04 % 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: -0.05 (0.44), residues: 383 helix: 0.38 (0.31), residues: 307 sheet: None (None), residues: 0 loop : -1.35 (0.73), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.009 0.001 PHE A 27 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1072.44 seconds wall clock time: 22 minutes 2.19 seconds (1322.19 seconds total)