Starting phenix.real_space_refine on Fri Jul 19 00:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/07_2024/8wqd_37740.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/07_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_37740/07_2024/8wqd_37740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/07_2024/8wqd_37740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/07_2024/8wqd_37740.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqd_37740/07_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-5388/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: 6.04, per 1000 atoms: 1.20 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: 1.98 Conformation dependent library (CDL) restraints added in 896.7 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: 0.54 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: 1.73 Time building geometry restraints manager: 2.20 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 2.440 nonbonded pdb=" OH TYR D 449 " pdb=" O PRO D 497 " model vdw 2.267 2.440 nonbonded pdb=" OE2 GLU D 2 " pdb=" OH TYR D 38 " model vdw 2.318 2.440 nonbonded pdb=" NH2 ARG D 126 " pdb=" O SER G -2 " model vdw 2.323 2.520 nonbonded pdb=" OG SER D 28 " pdb=" OD2 ASP D 31 " model vdw 2.327 2.440 ... (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 ========== 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: 12.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 22.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- 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 : 0.570 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: 0.1621 time to fit residues: 20.7534 Evaluate side-chains 60 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5133 Z= 0.230 Angle : 0.509 7.028 6955 Z= 0.270 Chirality : 0.038 0.123 804 Planarity : 0.004 0.046 902 Dihedral : 4.108 25.932 698 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.09 % Allowed : 10.20 % Favored : 88.71 % 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: -0.04 (0.35), residues: 635 helix: 0.68 (0.26), residues: 405 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 230 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 0.020 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 *********************** 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 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8409 (t80) cc_final: 0.7911 (t80) REVERT: D 472 TYR cc_start: 0.7305 (t80) cc_final: 0.7071 (t80) REVERT: D 517 LEU cc_start: 0.8992 (tp) cc_final: 0.8780 (tp) REVERT: D 622 GLU cc_start: 0.6975 (mp0) cc_final: 0.6729 (mp0) REVERT: G -18 ASP cc_start: 0.8094 (t0) cc_final: 0.7752 (t0) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.1409 time to fit residues: 13.7580 Evaluate side-chains 63 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1285 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= 0.199 Angle : 0.473 6.203 6955 Z= 0.251 Chirality : 0.037 0.126 804 Planarity : 0.004 0.046 902 Dihedral : 3.975 28.114 698 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.82 % Allowed : 12.93 % 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: 0.19 (0.35), residues: 635 helix: 0.87 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.24 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.002 0.001 HIS D 537 PHE 0.008 0.001 PHE D 101 TYR 0.018 0.001 TYR D 472 ARG 0.001 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 73 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8381 (t80) cc_final: 0.7866 (t80) REVERT: D 280 MET cc_start: 0.7767 (tmm) cc_final: 0.7035 (tmm) REVERT: D 419 GLU cc_start: 0.8080 (tp30) cc_final: 0.7854 (tp30) REVERT: D 472 TYR cc_start: 0.7321 (t80) cc_final: 0.6948 (t80) REVERT: D 517 LEU cc_start: 0.8930 (tp) cc_final: 0.8729 (tp) REVERT: D 622 GLU cc_start: 0.6920 (mp0) cc_final: 0.6706 (mp0) REVERT: G -18 ASP cc_start: 0.8119 (t0) cc_final: 0.7745 (t0) outliers start: 10 outliers final: 10 residues processed: 68 average time/residue: 0.1393 time to fit residues: 13.1994 Evaluate side-chains 66 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 420 GLN 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: 0.4980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1417 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= 0.247 Angle : 0.496 6.767 6955 Z= 0.263 Chirality : 0.038 0.132 804 Planarity : 0.004 0.044 902 Dihedral : 4.007 28.773 698 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.37 % Allowed : 15.30 % Favored : 82.33 % 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: 0.23 (0.35), residues: 635 helix: 0.92 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.26 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.002 0.001 HIS D 369 PHE 0.008 0.001 PHE D 388 TYR 0.016 0.001 TYR D 472 ARG 0.002 0.000 ARG D 424 *********************** 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 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8446 (t80) cc_final: 0.7920 (t80) REVERT: D 280 MET cc_start: 0.7827 (tmm) cc_final: 0.7100 (tmm) REVERT: D 472 TYR cc_start: 0.7366 (t80) cc_final: 0.6943 (t80) REVERT: D 517 LEU cc_start: 0.8963 (tp) cc_final: 0.8727 (tp) REVERT: D 622 GLU cc_start: 0.6910 (mp0) cc_final: 0.6706 (mp0) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.1394 time to fit residues: 12.9310 Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 507 CYS 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: 0.2980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 31 optimal weight: 0.0770 chunk 54 optimal weight: 0.0040 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.2468 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1501 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= 0.138 Angle : 0.447 6.335 6955 Z= 0.238 Chirality : 0.036 0.126 804 Planarity : 0.004 0.047 902 Dihedral : 3.803 28.821 698 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.82 % Allowed : 17.12 % Favored : 81.06 % 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: 1.15 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.002 0.000 HIS D 537 PHE 0.007 0.001 PHE D 101 TYR 0.016 0.001 TYR D 472 ARG 0.001 0.000 ARG D 424 *********************** 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 73 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8309 (t80) cc_final: 0.7741 (t80) REVERT: D 280 MET cc_start: 0.7836 (tmm) cc_final: 0.7108 (tmt) REVERT: D 472 TYR cc_start: 0.7268 (t80) cc_final: 0.6723 (t80) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.1444 time to fit residues: 14.0191 Evaluate side-chains 65 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 420 GLN 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 620 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5133 Z= 0.179 Angle : 0.469 7.069 6955 Z= 0.247 Chirality : 0.037 0.133 804 Planarity : 0.004 0.046 902 Dihedral : 3.783 28.738 698 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.82 % Allowed : 17.85 % Favored : 80.33 % 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: 0.57 (0.35), residues: 635 helix: 1.21 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.18 (0.44), residues: 223 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 0.008 0.001 PHE D 101 TYR 0.014 0.001 TYR D 472 ARG 0.002 0.000 ARG D 424 *********************** 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 71 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.549 Fit side-chains REVERT: D 172 TYR cc_start: 0.8352 (t80) cc_final: 0.7892 (t80) REVERT: D 280 MET cc_start: 0.7814 (tmm) cc_final: 0.7071 (tmm) REVERT: D 368 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (mp) REVERT: D 472 TYR cc_start: 0.7324 (t80) cc_final: 0.6720 (t80) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.1436 time to fit residues: 13.4991 Evaluate side-chains 64 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 D residue 620 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5133 Z= 0.145 Angle : 0.457 6.595 6955 Z= 0.240 Chirality : 0.036 0.134 804 Planarity : 0.004 0.047 902 Dihedral : 3.679 27.973 698 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.55 % Allowed : 17.67 % Favored : 79.78 % 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: 0.62 (0.36), residues: 635 helix: 1.25 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.002 0.000 HIS D 476 PHE 0.009 0.001 PHE D 101 TYR 0.014 0.001 TYR D 472 ARG 0.001 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 75 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8307 (t80) cc_final: 0.7767 (t80) REVERT: D 280 MET cc_start: 0.7766 (tmm) cc_final: 0.7089 (tmm) REVERT: D 288 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6272 (p0) REVERT: D 368 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8265 (mp) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.1291 time to fit residues: 12.9610 Evaluate side-chains 72 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 ASN 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 288 ASP Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 420 GLN 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 620 LEU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.3564 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5133 Z= 0.161 Angle : 0.463 6.595 6955 Z= 0.245 Chirality : 0.037 0.143 804 Planarity : 0.004 0.046 902 Dihedral : 3.653 26.586 698 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.73 % Allowed : 18.03 % 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: 0.62 (0.35), residues: 635 helix: 1.25 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.17 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 93 HIS 0.003 0.000 HIS D 476 PHE 0.010 0.001 PHE D 193 TYR 0.016 0.001 TYR D 472 ARG 0.001 0.000 ARG D 424 *********************** 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 73 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8315 (t80) cc_final: 0.7723 (t80) REVERT: D 280 MET cc_start: 0.7766 (tmm) cc_final: 0.7110 (tmm) REVERT: D 368 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8289 (mp) REVERT: D 472 TYR cc_start: 0.7126 (t80) cc_final: 0.6689 (t80) REVERT: G -18 ASP cc_start: 0.8102 (t0) cc_final: 0.7795 (t0) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.1309 time to fit residues: 12.8635 Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 ASN 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 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 620 LEU 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: 0.6980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5133 Z= 0.228 Angle : 0.494 6.233 6955 Z= 0.259 Chirality : 0.038 0.129 804 Planarity : 0.004 0.044 902 Dihedral : 3.768 24.264 698 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.55 % Allowed : 17.85 % 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: 0.55 (0.35), residues: 635 helix: 1.19 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.18 (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 0.011 0.001 PHE D 101 TYR 0.015 0.001 TYR D 472 ARG 0.002 0.000 ARG D 424 *********************** 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 73 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.668 Fit side-chains REVERT: D 172 TYR cc_start: 0.8391 (t80) cc_final: 0.7828 (t80) REVERT: D 280 MET cc_start: 0.7834 (tmm) cc_final: 0.7134 (tmm) REVERT: D 368 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 472 TYR cc_start: 0.7260 (t80) cc_final: 0.6846 (t80) REVERT: G -18 ASP cc_start: 0.8119 (t0) cc_final: 0.7796 (t0) outliers start: 14 outliers final: 11 residues processed: 70 average time/residue: 0.1397 time to fit residues: 14.2286 Evaluate side-chains 67 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 ASN 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 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1720 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= 0.206 Angle : 0.491 7.056 6955 Z= 0.257 Chirality : 0.038 0.144 804 Planarity : 0.004 0.045 902 Dihedral : 3.748 23.780 698 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.55 % Allowed : 18.03 % Favored : 79.42 % 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: 0.55 (0.35), residues: 635 helix: 1.17 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.15 (0.45), residues: 221 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 0.001 0.000 ARG D 424 ********************** 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 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.564 Fit side-chains REVERT: D 172 TYR cc_start: 0.8387 (t80) cc_final: 0.7838 (t80) REVERT: D 280 MET cc_start: 0.7890 (tmm) cc_final: 0.7191 (tmt) REVERT: D 368 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 472 TYR cc_start: 0.7260 (t80) cc_final: 0.6863 (t80) REVERT: G -18 ASP cc_start: 0.8151 (t0) cc_final: 0.7840 (t0) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 0.1334 time to fit residues: 12.7763 Evaluate side-chains 70 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 ASN 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 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 2 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.2702 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117960 restraints weight = 6767.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119820 restraints weight = 10714.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121302 restraints weight = 7208.820| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 5133 Z= 0.251 Angle : 1.072 59.176 6955 Z= 0.636 Chirality : 0.045 0.735 804 Planarity : 0.004 0.052 902 Dihedral : 3.907 29.705 698 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.55 % Allowed : 18.58 % Favored : 78.87 % Cbeta Deviations : 0.16 % 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: 0.55 (0.35), residues: 635 helix: 1.17 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 221 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 0.011 0.001 PHE D 447 TYR 0.015 0.001 TYR D 472 ARG 0.001 0.000 ARG D 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.83 seconds wall clock time: 32 minutes 15.27 seconds (1935.27 seconds total)