Starting phenix.real_space_refine on Fri Aug 2 20:33:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/08_2024/8wqd_37740.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 29 5.16 5 C 3166 2.51 5 N 905 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 268": "OD1" <-> "OD2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP -18": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5046 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain breaks: 1 Time building chain proxies: 5.54, per 1000 atoms: 1.10 Number of scatterers: 5046 At special positions: 0 Unit cell: (104.14, 98.4, 85.28, 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 29 16.00 O 946 8.00 N 905 7.00 C 3166 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: 1.86 Conformation dependent library (CDL) restraints added in 925.4 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 66.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'D' and resid 1 through 14 removed outlier: 3.707A pdb=" N ALA D 5 " --> pdb=" O MET D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 28 through 38 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.857A pdb=" N HIS D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.860A pdb=" N LEU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.598A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 189 through 198 removed outlier: 4.098A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.520A pdb=" N VAL D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 246 through 262 Processing helix chain 'D' and resid 269 through 285 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.502A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 337 removed outlier: 3.616A pdb=" N LEU D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 382 through 398 removed outlier: 3.765A pdb=" N LEU D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 428 Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 460 through 478 Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.760A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 3.963A pdb=" N ILE D 555 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 559 " --> pdb=" O ILE D 555 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 591 Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.833A pdb=" N ASN D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 4.179A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'G' and resid -21 through -17 removed outlier: 3.622A pdb=" N ASP G -18 " --> pdb=" O HIS G -21 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G -17 " --> pdb=" O SER G -20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid -21 through -17' Processing sheet with id=AA1, first strand: chain 'D' and resid 40 through 41 260 hydrogen bonds defined for protein. 762 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: 1.49 Time building geometry restraints manager: 2.08 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: 1721 1.34 - 1.46: 768 1.46 - 1.57: 2603 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 5133 Sorted by residual: bond pdb=" C ALA D 404 " pdb=" N PRO D 405 " ideal model delta sigma weight residual 1.335 1.364 -0.030 1.28e-02 6.10e+03 5.37e+00 bond pdb=" CB ILE D 555 " pdb=" CG2 ILE D 555 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CA GLU D 307 " pdb=" CB GLU D 307 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.86e-02 2.89e+03 1.08e+00 bond pdb=" CB PHE D 388 " pdb=" CG PHE D 388 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.07e+00 bond pdb=" CA ILE D 616 " pdb=" CB ILE D 616 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.01e+00 ... (remaining 5128 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 100 106.39 - 113.29: 2886 113.29 - 120.19: 1834 120.19 - 127.09: 2088 127.09 - 133.99: 47 Bond angle restraints: 6955 Sorted by residual: angle pdb=" C ASN D 289 " pdb=" CA ASN D 289 " pdb=" CB ASN D 289 " ideal model delta sigma weight residual 116.54 111.16 5.38 1.15e+00 7.56e-01 2.19e+01 angle pdb=" N ASP G -18 " pdb=" CA ASP G -18 " pdb=" C ASP G -18 " ideal model delta sigma weight residual 114.75 109.27 5.48 1.26e+00 6.30e-01 1.89e+01 angle pdb=" N THR D 306 " pdb=" CA THR D 306 " pdb=" C THR D 306 " ideal model delta sigma weight residual 111.55 107.45 4.10 1.37e+00 5.33e-01 8.96e+00 angle pdb=" CA ASN D 289 " pdb=" C ASN D 289 " pdb=" N ILE D 290 " ideal model delta sigma weight residual 119.52 117.24 2.28 7.90e-01 1.60e+00 8.31e+00 angle pdb=" CA ASP G -18 " pdb=" C ASP G -18 " pdb=" N LEU G -17 " ideal model delta sigma weight residual 119.80 116.12 3.68 1.34e+00 5.57e-01 7.53e+00 ... (remaining 6950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 2744 16.80 - 33.60: 292 33.60 - 50.40: 57 50.40 - 67.19: 13 67.19 - 83.99: 4 Dihedral angle restraints: 3110 sinusoidal: 1231 harmonic: 1879 Sorted by residual: dihedral pdb=" CA ASP D 478 " pdb=" CB ASP D 478 " pdb=" CG ASP D 478 " pdb=" OD1 ASP D 478 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CB GLU D 586 " pdb=" CG GLU D 586 " pdb=" CD GLU D 586 " pdb=" OE1 GLU D 586 " ideal model delta sinusoidal sigma weight residual 0.00 83.99 -83.99 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CG ARG D 80 " pdb=" CD ARG D 80 " pdb=" NE ARG D 80 " pdb=" CZ ARG D 80 " ideal model delta sinusoidal sigma weight residual 180.00 138.50 41.50 2 1.50e+01 4.44e-03 9.37e+00 ... (remaining 3107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 426 0.029 - 0.057: 264 0.057 - 0.086: 81 0.086 - 0.115: 28 0.115 - 0.143: 5 Chirality restraints: 804 Sorted by residual: chirality pdb=" CG LEU D 238 " pdb=" CB LEU D 238 " pdb=" CD1 LEU D 238 " pdb=" CD2 LEU D 238 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE D 616 " pdb=" N ILE D 616 " pdb=" C ILE D 616 " pdb=" CB ILE D 616 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO D 576 " pdb=" N PRO D 576 " pdb=" C PRO D 576 " pdb=" CB PRO D 576 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 801 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 221 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 222 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 222 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 222 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 404 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO D 405 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 405 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 405 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 123 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO D 124 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.028 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1233 2.79 - 3.32: 4988 3.32 - 3.85: 8291 3.85 - 4.37: 9423 4.37 - 4.90: 16449 Nonbonded interactions: 40384 Sorted by model distance: nonbonded pdb=" O ASP D 87 " pdb=" OG1 THR D 118 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR D 449 " pdb=" O PRO D 497 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU D 2 " pdb=" OH TYR D 38 " model vdw 2.318 3.040 nonbonded pdb=" NH2 ARG D 126 " pdb=" O SER G -2 " model vdw 2.323 3.120 nonbonded pdb=" OG SER D 28 " pdb=" OD2 ASP D 31 " model vdw 2.327 3.040 ... (remaining 40379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.039 5133 Z= 0.276 Angle : 0.624 7.431 6955 Z= 0.344 Chirality : 0.041 0.143 804 Planarity : 0.005 0.056 902 Dihedral : 14.561 83.992 1892 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.33), residues: 635 helix: 0.05 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 93 HIS 0.005 0.001 HIS D 476 PHE 0.010 0.002 PHE D 388 TYR 0.013 0.001 TYR D 440 ARG 0.003 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.581 Fit side-chains REVERT: D 135 ASP cc_start: 0.8123 (m-30) cc_final: 0.7669 (m-30) REVERT: D 172 TYR cc_start: 0.8386 (t80) cc_final: 0.7901 (t80) REVERT: D 300 HIS cc_start: 0.7876 (t70) cc_final: 0.7500 (t70) REVERT: D 307 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 419 GLU cc_start: 0.7940 (tp30) cc_final: 0.7688 (tp30) REVERT: D 472 TYR cc_start: 0.7457 (t80) cc_final: 0.7171 (t80) REVERT: D 517 LEU cc_start: 0.8861 (tp) cc_final: 0.8642 (tp) REVERT: D 622 GLU cc_start: 0.6999 (mp0) cc_final: 0.6734 (mp0) REVERT: G -18 ASP cc_start: 0.8083 (t0) cc_final: 0.7827 (t0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1650 time to fit residues: 20.9548 Evaluate side-chains 60 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN D 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5133 Z= 0.244 Angle : 0.529 6.586 6955 Z= 0.281 Chirality : 0.039 0.136 804 Planarity : 0.005 0.047 902 Dihedral : 4.176 27.482 698 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.28 % Allowed : 9.84 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.14 (0.34), residues: 635 helix: 0.58 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.003 0.001 HIS D 100 PHE 0.009 0.001 PHE D 388 TYR 0.019 0.001 TYR D 472 ARG 0.004 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8429 (t80) cc_final: 0.8034 (t80) REVERT: D 280 MET cc_start: 0.7713 (tmm) cc_final: 0.6927 (tmm) REVERT: D 472 TYR cc_start: 0.7359 (t80) cc_final: 0.7127 (t80) REVERT: D 517 LEU cc_start: 0.9008 (tp) cc_final: 0.8795 (tp) REVERT: G -18 ASP cc_start: 0.8101 (t0) cc_final: 0.7772 (t0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1547 time to fit residues: 15.0305 Evaluate side-chains 65 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5133 Z= 0.251 Angle : 0.510 6.353 6955 Z= 0.271 Chirality : 0.039 0.132 804 Planarity : 0.004 0.047 902 Dihedral : 4.084 25.867 698 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.28 % Allowed : 13.48 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.01 (0.34), residues: 635 helix: 0.76 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.003 0.001 HIS D 100 PHE 0.009 0.001 PHE D 388 TYR 0.018 0.001 TYR D 472 ARG 0.003 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.598 Fit side-chains REVERT: D 172 TYR cc_start: 0.8457 (t80) cc_final: 0.8022 (t80) REVERT: D 280 MET cc_start: 0.7811 (tmm) cc_final: 0.7041 (tmm) REVERT: D 472 TYR cc_start: 0.7416 (t80) cc_final: 0.7063 (t80) REVERT: D 517 LEU cc_start: 0.9011 (tp) cc_final: 0.8789 (tp) REVERT: D 622 GLU cc_start: 0.6898 (mp0) cc_final: 0.6696 (mp0) REVERT: G -18 ASP cc_start: 0.8180 (t0) cc_final: 0.7848 (t0) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.1708 time to fit residues: 15.7324 Evaluate side-chains 62 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5133 Z= 0.217 Angle : 0.493 6.932 6955 Z= 0.263 Chirality : 0.038 0.131 804 Planarity : 0.004 0.047 902 Dihedral : 3.985 23.995 698 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.00 % Allowed : 15.30 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.35), residues: 635 helix: 0.93 (0.27), residues: 411 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.002 0.001 HIS D 382 PHE 0.009 0.001 PHE D 101 TYR 0.016 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8445 (t80) cc_final: 0.8011 (t80) REVERT: D 280 MET cc_start: 0.7851 (tmm) cc_final: 0.7079 (tmt) REVERT: D 472 TYR cc_start: 0.7353 (t80) cc_final: 0.6921 (t80) REVERT: D 517 LEU cc_start: 0.9010 (tp) cc_final: 0.8797 (tp) REVERT: D 622 GLU cc_start: 0.6852 (mp0) cc_final: 0.6650 (mp0) REVERT: G -18 ASP cc_start: 0.8184 (t0) cc_final: 0.7838 (t0) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1857 time to fit residues: 17.7202 Evaluate side-chains 67 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.4980 chunk 34 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 54 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5133 Z= 0.127 Angle : 0.443 5.862 6955 Z= 0.238 Chirality : 0.036 0.123 804 Planarity : 0.004 0.049 902 Dihedral : 3.668 22.609 698 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.64 % Allowed : 16.39 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.52 (0.35), residues: 635 helix: 1.21 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.002 0.000 HIS D 537 PHE 0.006 0.001 PHE D 101 TYR 0.016 0.001 TYR D 472 ARG 0.001 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8287 (t80) cc_final: 0.7721 (t80) REVERT: D 280 MET cc_start: 0.7824 (tmm) cc_final: 0.7034 (tmt) REVERT: G -18 ASP cc_start: 0.8144 (t0) cc_final: 0.7766 (t0) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1442 time to fit residues: 14.9238 Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5133 Z= 0.214 Angle : 0.494 7.016 6955 Z= 0.260 Chirality : 0.038 0.127 804 Planarity : 0.004 0.046 902 Dihedral : 3.770 22.108 698 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.00 % Allowed : 17.12 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.48 (0.35), residues: 635 helix: 1.17 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.008 0.001 PHE D 101 TYR 0.015 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8398 (t80) cc_final: 0.7919 (t80) REVERT: D 280 MET cc_start: 0.7841 (tmm) cc_final: 0.7054 (tmm) REVERT: D 368 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8295 (mp) REVERT: D 472 TYR cc_start: 0.7252 (t80) cc_final: 0.6827 (t80) REVERT: G -18 ASP cc_start: 0.8192 (t0) cc_final: 0.7802 (t0) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1373 time to fit residues: 12.2392 Evaluate side-chains 62 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.2980 chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5133 Z= 0.204 Angle : 0.485 7.160 6955 Z= 0.256 Chirality : 0.038 0.134 804 Planarity : 0.004 0.047 902 Dihedral : 3.766 20.525 698 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.00 % Allowed : 17.12 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.50 (0.35), residues: 635 helix: 1.17 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.009 0.001 PHE D 101 TYR 0.016 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8391 (t80) cc_final: 0.7932 (t80) REVERT: D 280 MET cc_start: 0.7899 (tmm) cc_final: 0.7104 (tmt) REVERT: D 368 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (mp) REVERT: G -18 ASP cc_start: 0.8174 (t0) cc_final: 0.7774 (t0) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1584 time to fit residues: 14.9218 Evaluate side-chains 61 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN D 262 ASN D 504 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5133 Z= 0.217 Angle : 0.499 7.415 6955 Z= 0.264 Chirality : 0.038 0.148 804 Planarity : 0.004 0.047 902 Dihedral : 3.819 20.245 698 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.00 % Allowed : 18.40 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.45 (0.35), residues: 635 helix: 1.13 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -1.24 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.010 0.001 PHE D 101 TYR 0.016 0.001 TYR D 472 ARG 0.003 0.000 ARG D 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8401 (t80) cc_final: 0.7883 (t80) REVERT: D 280 MET cc_start: 0.7917 (tmm) cc_final: 0.7148 (tmt) REVERT: D 368 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8261 (mp) REVERT: D 472 TYR cc_start: 0.7282 (t80) cc_final: 0.6898 (t80) REVERT: G -18 ASP cc_start: 0.8190 (t0) cc_final: 0.7788 (t0) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.1330 time to fit residues: 11.5793 Evaluate side-chains 62 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.028 5133 Z= 0.201 Angle : 0.499 7.385 6955 Z= 0.262 Chirality : 0.038 0.155 804 Planarity : 0.004 0.047 902 Dihedral : 3.799 19.723 698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.00 % Allowed : 19.13 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.42 (0.35), residues: 635 helix: 1.11 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.010 0.001 PHE D 101 TYR 0.014 0.001 TYR D 472 ARG 0.002 0.000 ARG D 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8396 (t80) cc_final: 0.7887 (t80) REVERT: D 280 MET cc_start: 0.7920 (tmm) cc_final: 0.7154 (tmt) REVERT: D 368 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (mp) REVERT: D 472 TYR cc_start: 0.7247 (t80) cc_final: 0.6832 (t80) REVERT: G -18 ASP cc_start: 0.8188 (t0) cc_final: 0.7785 (t0) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1483 time to fit residues: 13.8816 Evaluate side-chains 63 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 369 HIS D 504 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5133 Z= 0.219 Angle : 0.511 7.141 6955 Z= 0.267 Chirality : 0.038 0.146 804 Planarity : 0.004 0.047 902 Dihedral : 3.814 19.889 698 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.19 % Allowed : 18.58 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.41 (0.35), residues: 635 helix: 1.11 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.013 0.001 PHE D 193 TYR 0.024 0.001 TYR D 163 ARG 0.005 0.000 ARG D 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8409 (t80) cc_final: 0.7886 (t80) REVERT: D 280 MET cc_start: 0.7917 (tmm) cc_final: 0.7160 (tmt) REVERT: D 368 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8266 (mp) REVERT: D 472 TYR cc_start: 0.7237 (t80) cc_final: 0.6811 (t80) REVERT: G -18 ASP cc_start: 0.8190 (t0) cc_final: 0.7790 (t0) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.1298 time to fit residues: 11.4758 Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131518 restraints weight = 6658.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131470 restraints weight = 9357.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132413 restraints weight = 8337.927| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5133 Z= 0.174 Angle : 0.495 6.531 6955 Z= 0.259 Chirality : 0.038 0.134 804 Planarity : 0.004 0.047 902 Dihedral : 3.754 19.427 698 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 18.76 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.45 (0.35), residues: 635 helix: 1.13 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.003 0.000 HIS D 476 PHE 0.012 0.001 PHE D 193 TYR 0.023 0.001 TYR D 163 ARG 0.004 0.000 ARG D 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.94 seconds wall clock time: 33 minutes 36.13 seconds (2016.13 seconds total)