Starting phenix.real_space_refine on Fri Apr 5 14:35:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhr_36285/04_2024/8jhr_36285_updated.pdb" } resolution = 3.52 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= -0.002 sd= 0.048 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 19 5.16 5 C 2166 2.51 5 N 548 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 14, 'TRANS': 415} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.70 Number of scatterers: 3302 At special positions: 0 Unit cell: (85.85, 60.35, 66.3, 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 19 16.00 O 569 8.00 N 548 7.00 C 2166 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: 1.38 Conformation dependent library (CDL) restraints added in 613.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 99 through 133 removed outlier: 4.753A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 4.095A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.819A pdb=" N SER A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 221 Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 224 through 256 removed outlier: 4.189A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.542A pdb=" N GLY A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.867A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 349 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 390 removed outlier: 4.050A pdb=" N PHE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.972A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 4.833A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.659A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N THR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 494 through 536 removed outlier: 4.495A pdb=" N LEU A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.687A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1004 1.34 - 1.46: 626 1.46 - 1.58: 1717 1.58 - 1.69: 5 1.69 - 1.81: 28 Bond restraints: 3380 Sorted by residual: bond pdb=" C07 YUX A 601 " pdb=" N06 YUX A 601 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C07 YUX A 601 " pdb=" C08 YUX A 601 " ideal model delta sigma weight residual 1.534 1.611 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C22 YUX A 601 " pdb=" C23 YUX A 601 " ideal model delta sigma weight residual 1.387 1.452 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C08 YUX A 601 " pdb=" C23 YUX A 601 " ideal model delta sigma weight residual 1.386 1.451 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C11 YUX A 601 " pdb=" C22 YUX A 601 " ideal model delta sigma weight residual 1.386 1.451 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3375 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.84: 57 105.84 - 112.91: 1815 112.91 - 119.98: 1218 119.98 - 127.05: 1460 127.05 - 134.12: 41 Bond angle restraints: 4591 Sorted by residual: angle pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" C VAL A 265 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" C THR A 352 " pdb=" N CYS A 353 " pdb=" CA CYS A 353 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" N GLU A 351 " pdb=" CA GLU A 351 " pdb=" C GLU A 351 " ideal model delta sigma weight residual 113.18 108.89 4.29 1.33e+00 5.65e-01 1.04e+01 angle pdb=" C GLY A 162 " pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta sigma weight residual 121.14 115.63 5.51 1.75e+00 3.27e-01 9.93e+00 angle pdb=" C ASP A 163 " pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 122.09 116.49 5.60 1.79e+00 3.12e-01 9.78e+00 ... (remaining 4586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.66: 1693 19.66 - 39.32: 190 39.32 - 58.98: 52 58.98 - 78.64: 6 78.64 - 98.30: 3 Dihedral angle restraints: 1944 sinusoidal: 723 harmonic: 1221 Sorted by residual: dihedral pdb=" C16 YUX A 601 " pdb=" C17 YUX A 601 " pdb=" C18 YUX A 601 " pdb=" C19 YUX A 601 " ideal model delta sinusoidal sigma weight residual 190.18 91.88 98.30 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" CA ALA A 350 " pdb=" C ALA A 350 " pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG A 299 " pdb=" CD ARG A 299 " pdb=" NE ARG A 299 " pdb=" CZ ARG A 299 " ideal model delta sinusoidal sigma weight residual -180.00 -136.42 -43.58 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 441 0.054 - 0.107: 78 0.107 - 0.161: 14 0.161 - 0.214: 1 0.214 - 0.268: 3 Chirality restraints: 537 Sorted by residual: chirality pdb=" CG LEU A 413 " pdb=" CB LEU A 413 " pdb=" CD1 LEU A 413 " pdb=" CD2 LEU A 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU A 499 " pdb=" CB LEU A 499 " pdb=" CD1 LEU A 499 " pdb=" CD2 LEU A 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 373 " pdb=" CA THR A 373 " pdb=" OG1 THR A 373 " pdb=" CG2 THR A 373 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 534 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.015 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP A 178 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 136 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LYS A 136 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 136 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 137 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 214 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 215 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.024 5.00e-02 4.00e+02 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 423 2.75 - 3.28: 3506 3.28 - 3.82: 5708 3.82 - 4.36: 5978 4.36 - 4.90: 10790 Nonbonded interactions: 26405 Sorted by model distance: nonbonded pdb=" O VAL A 346 " pdb=" OG1 THR A 349 " model vdw 2.208 2.440 nonbonded pdb=" O VAL A 537 " pdb=" ND2 ASN A 538 " model vdw 2.270 2.520 nonbonded pdb=" O MET A 448 " pdb=" NH1 ARG A 456 " model vdw 2.278 2.520 nonbonded pdb=" O ILE A 213 " pdb=" OG1 THR A 216 " model vdw 2.282 2.440 nonbonded pdb=" O TRP A 178 " pdb=" OG1 THR A 182 " model vdw 2.297 2.440 ... (remaining 26400 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: 1.900 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: 5.580 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.006 0.110 3380 Z= 0.344 Angle : 0.778 9.441 4591 Z= 0.393 Chirality : 0.046 0.268 537 Planarity : 0.004 0.043 563 Dihedral : 17.684 98.304 1164 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.29 % Allowed : 35.26 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.42), residues: 426 helix: 1.60 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.44 (0.90), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.002 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.006 0.001 TYR A 246 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.391 Fit side-chains REVERT: A 306 MET cc_start: 0.8527 (mmm) cc_final: 0.7927 (mmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.1692 time to fit residues: 12.8925 Evaluate side-chains 64 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3380 Z= 0.160 Angle : 0.548 5.949 4591 Z= 0.289 Chirality : 0.040 0.174 537 Planarity : 0.004 0.038 563 Dihedral : 6.234 58.175 477 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.05 % Allowed : 31.79 % Favored : 64.16 % 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: 2.31 (0.42), residues: 426 helix: 1.92 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.08 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.022 0.001 PHE A 510 TYR 0.026 0.001 TYR A 160 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.330 Fit side-chains REVERT: A 455 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8220 (ptt-90) REVERT: A 532 ARG cc_start: 0.9107 (tpp80) cc_final: 0.8840 (tpp80) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.1736 time to fit residues: 17.5298 Evaluate side-chains 83 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3380 Z= 0.185 Angle : 0.544 6.507 4591 Z= 0.291 Chirality : 0.041 0.190 537 Planarity : 0.004 0.036 563 Dihedral : 6.085 58.244 477 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.36 % Allowed : 30.64 % Favored : 63.01 % 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: 2.34 (0.42), residues: 426 helix: 1.93 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.02 (0.97), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.011 0.001 PHE A 327 TYR 0.014 0.001 TYR A 160 ARG 0.001 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8503 (mm) outliers start: 22 outliers final: 14 residues processed: 88 average time/residue: 0.1473 time to fit residues: 15.8941 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0010 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4464 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3380 Z= 0.168 Angle : 0.543 6.117 4591 Z= 0.287 Chirality : 0.040 0.198 537 Planarity : 0.003 0.034 563 Dihedral : 5.877 54.622 477 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.07 % Allowed : 30.35 % Favored : 63.58 % 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: 2.38 (0.43), residues: 426 helix: 1.97 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.02 (0.98), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.028 0.001 PHE A 510 TYR 0.009 0.001 TYR A 192 ARG 0.002 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8456 (mm) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 0.1472 time to fit residues: 16.0233 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3380 Z= 0.169 Angle : 0.576 8.435 4591 Z= 0.296 Chirality : 0.040 0.157 537 Planarity : 0.004 0.035 563 Dihedral : 5.720 51.430 477 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.36 % Allowed : 30.06 % Favored : 63.58 % 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: 2.41 (0.42), residues: 426 helix: 1.96 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.88 (0.99), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 498 TYR 0.010 0.001 TYR A 192 ARG 0.001 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 332 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8443 (mm) outliers start: 22 outliers final: 15 residues processed: 79 average time/residue: 0.1552 time to fit residues: 15.2291 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3380 Z= 0.214 Angle : 0.586 7.325 4591 Z= 0.307 Chirality : 0.041 0.152 537 Planarity : 0.004 0.033 563 Dihedral : 5.789 52.840 477 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.36 % Allowed : 29.77 % Favored : 63.87 % 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: 2.33 (0.43), residues: 426 helix: 1.91 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.92 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.031 0.002 PHE A 510 TYR 0.016 0.001 TYR A 160 ARG 0.005 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.329 Fit side-chains REVERT: A 218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 332 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8503 (mm) outliers start: 22 outliers final: 16 residues processed: 79 average time/residue: 0.1490 time to fit residues: 14.3867 Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3380 Z= 0.220 Angle : 0.608 7.193 4591 Z= 0.316 Chirality : 0.042 0.219 537 Planarity : 0.004 0.038 563 Dihedral : 5.800 51.905 477 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.07 % Allowed : 30.92 % Favored : 63.01 % 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: 2.24 (0.42), residues: 426 helix: 1.86 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.98 (0.99), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 178 HIS 0.002 0.001 HIS A 260 PHE 0.013 0.001 PHE A 327 TYR 0.009 0.001 TYR A 192 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 332 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8492 (mm) outliers start: 21 outliers final: 18 residues processed: 76 average time/residue: 0.1548 time to fit residues: 14.3636 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3380 Z= 0.171 Angle : 0.585 6.586 4591 Z= 0.301 Chirality : 0.041 0.194 537 Planarity : 0.004 0.033 563 Dihedral : 5.575 45.688 477 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.78 % Allowed : 31.50 % Favored : 62.72 % 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: 2.37 (0.43), residues: 426 helix: 1.95 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.93 (0.99), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.001 0.001 HIS A 260 PHE 0.029 0.001 PHE A 510 TYR 0.017 0.001 TYR A 160 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 306 MET cc_start: 0.8513 (mmm) cc_final: 0.8009 (mmm) REVERT: A 332 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8468 (mm) outliers start: 20 outliers final: 16 residues processed: 74 average time/residue: 0.1429 time to fit residues: 13.2342 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4832 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3380 Z= 0.178 Angle : 0.600 8.574 4591 Z= 0.308 Chirality : 0.041 0.194 537 Planarity : 0.004 0.032 563 Dihedral : 5.483 45.262 477 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.20 % Allowed : 31.79 % Favored : 63.01 % 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: 2.40 (0.43), residues: 426 helix: 1.97 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.93 (0.98), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 151 TYR 0.008 0.001 TYR A 192 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 332 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8488 (mm) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.1492 time to fit residues: 13.5575 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3380 Z= 0.178 Angle : 0.632 12.769 4591 Z= 0.316 Chirality : 0.041 0.191 537 Planarity : 0.004 0.034 563 Dihedral : 5.051 44.392 475 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.78 % Allowed : 31.50 % Favored : 62.72 % 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: 2.33 (0.43), residues: 426 helix: 1.91 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.90 (0.98), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.032 0.001 PHE A 510 TYR 0.018 0.001 TYR A 160 ARG 0.002 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 332 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 462 LEU cc_start: 0.7747 (tp) cc_final: 0.7526 (tp) outliers start: 20 outliers final: 16 residues processed: 74 average time/residue: 0.1427 time to fit residues: 13.1756 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 440 TRP Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0040 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.3730 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.159177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129994 restraints weight = 4918.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.133845 restraints weight = 2739.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136436 restraints weight = 1921.510| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3380 Z= 0.171 Angle : 0.649 11.969 4591 Z= 0.322 Chirality : 0.041 0.185 537 Planarity : 0.004 0.032 563 Dihedral : 4.911 40.576 475 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.78 % Allowed : 32.08 % Favored : 62.14 % 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: 2.39 (0.43), residues: 426 helix: 1.96 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.81 (0.96), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.001 0.001 HIS A 132 PHE 0.013 0.001 PHE A 519 TYR 0.011 0.001 TYR A 192 ARG 0.002 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.84 seconds wall clock time: 21 minutes 46.85 seconds (1306.85 seconds total)