Starting phenix.real_space_refine on Fri Apr 5 15:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc4_40337/04_2024/8sc4_40337_updated.pdb" } resolution = 3.46 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= 0.015 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 31 5.16 5 C 2335 2.51 5 N 579 2.21 5 O 599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3535 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.58, per 1000 atoms: 0.73 Number of scatterers: 3544 At special positions: 0 Unit cell: (88.803, 81.972, 67.4561, 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 31 16.00 O 599 8.00 N 579 7.00 C 2335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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: 1.39 Conformation dependent library (CDL) restraints added in 757.6 milliseconds 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 74.3% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 4.356A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix removed outlier: 5.154A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 66 through 72 removed outlier: 4.048A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 72' Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.322A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 154 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.942A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 4.152A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 257 removed outlier: 4.439A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 279 Proline residue: A 271 - end of helix removed outlier: 3.680A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 341 through 371 Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.666A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.580A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 3.580A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.824A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= B, first strand: chain 'A' and resid 89 through 91 221 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1089 1.35 - 1.46: 929 1.46 - 1.58: 1575 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 3639 Sorted by residual: bond pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.317 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.354 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.314 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 1.284 1.316 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 3634 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 119 106.25 - 113.19: 1926 113.19 - 120.13: 1354 120.13 - 127.07: 1512 127.07 - 134.01: 52 Bond angle restraints: 4963 Sorted by residual: angle pdb=" C LEU A 180 " pdb=" N GLY A 181 " pdb=" CA GLY A 181 " ideal model delta sigma weight residual 119.94 122.86 -2.92 1.11e+00 8.12e-01 6.93e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.31 -5.91 2.30e+00 1.89e-01 6.60e+00 angle pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" C GLN A 241 " ideal model delta sigma weight residual 111.07 108.38 2.69 1.07e+00 8.73e-01 6.34e+00 angle pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.54 123.86 -3.32 1.35e+00 5.49e-01 6.06e+00 angle pdb=" CA GLN A 241 " pdb=" C GLN A 241 " pdb=" O GLN A 241 " ideal model delta sigma weight residual 120.82 118.35 2.47 1.05e+00 9.07e-01 5.52e+00 ... (remaining 4958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1938 14.28 - 28.56: 130 28.56 - 42.84: 35 42.84 - 57.12: 5 57.12 - 71.40: 2 Dihedral angle restraints: 2110 sinusoidal: 804 harmonic: 1306 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -47.29 -38.71 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA SER A 424 " pdb=" C SER A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 -165.86 -14.14 0 5.00e+00 4.00e-02 8.00e+00 dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -165.96 -14.04 0 5.00e+00 4.00e-02 7.88e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 361 0.033 - 0.066: 159 0.066 - 0.099: 41 0.099 - 0.132: 12 0.132 - 0.165: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PRO A 286 " pdb=" N PRO A 286 " pdb=" C PRO A 286 " pdb=" CB PRO A 286 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 571 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -1.308 2.00e-02 2.50e+03 6.51e-01 9.54e+03 pdb=" C03 MF8 A 601 " 1.075 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.093 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.035 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.105 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.321 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.546 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.721 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET A 406 " 0.041 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C THR A 182 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.013 2.00e-02 2.50e+03 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 972 2.82 - 3.34: 3710 3.34 - 3.86: 5965 3.86 - 4.38: 6756 4.38 - 4.90: 11471 Nonbonded interactions: 28874 Sorted by model distance: nonbonded pdb=" OG SER A 196 " pdb=" OG SER A 201 " model vdw 2.296 2.440 nonbonded pdb=" NH1 ARG A 175 " pdb=" O LEU A 290 " model vdw 2.334 2.520 nonbonded pdb=" O VAL A 74 " pdb=" NH2 ARG A 113 " model vdw 2.385 2.520 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.437 2.440 nonbonded pdb=" O ALA A 506 " pdb=" OG1 THR A 510 " model vdw 2.472 2.440 ... (remaining 28869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 3.580 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 0.041 3639 Z= 0.235 Angle : 0.683 6.073 4963 Z= 0.390 Chirality : 0.039 0.165 574 Planarity : 0.027 0.651 613 Dihedral : 10.980 71.396 1265 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.38), residues: 452 helix: -0.84 (0.26), residues: 329 sheet: None (None), residues: 0 loop : 0.59 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 288 HIS 0.003 0.001 HIS A 48 PHE 0.032 0.002 PHE A 173 TYR 0.012 0.002 TYR A 168 ARG 0.006 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8553 (p) cc_final: 0.8200 (m) REVERT: A 218 MET cc_start: 0.7252 (mmm) cc_final: 0.6998 (mmt) REVERT: A 346 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7634 (mtt90) REVERT: A 378 ASP cc_start: 0.7707 (m-30) cc_final: 0.7330 (m-30) REVERT: A 418 LEU cc_start: 0.8570 (tp) cc_final: 0.8242 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1571 time to fit residues: 23.0762 Evaluate side-chains 86 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3639 Z= 0.196 Angle : 0.690 16.498 4963 Z= 0.325 Chirality : 0.040 0.220 574 Planarity : 0.005 0.072 613 Dihedral : 4.436 16.935 491 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.63 % Allowed : 11.05 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.42), residues: 452 helix: 1.15 (0.30), residues: 327 sheet: None (None), residues: 0 loop : 1.49 (0.66), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 367 PHE 0.021 0.002 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.007 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.375 Fit side-chains REVERT: A 22 PHE cc_start: 0.6224 (t80) cc_final: 0.5783 (t80) REVERT: A 121 CYS cc_start: 0.5724 (OUTLIER) cc_final: 0.5317 (m) REVERT: A 132 SER cc_start: 0.8520 (p) cc_final: 0.8093 (m) REVERT: A 218 MET cc_start: 0.7340 (mmm) cc_final: 0.6970 (mmt) REVERT: A 234 ARG cc_start: 0.6432 (ttm170) cc_final: 0.5901 (ptt180) REVERT: A 346 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7542 (mtt90) REVERT: A 378 ASP cc_start: 0.7496 (m-30) cc_final: 0.7274 (m-30) REVERT: A 418 LEU cc_start: 0.8486 (tp) cc_final: 0.8130 (tp) REVERT: A 448 MET cc_start: 0.8637 (mmm) cc_final: 0.8241 (mmm) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.1451 time to fit residues: 17.9504 Evaluate side-chains 85 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3639 Z= 0.175 Angle : 0.649 14.640 4963 Z= 0.302 Chirality : 0.038 0.172 574 Planarity : 0.004 0.056 613 Dihedral : 4.205 19.902 491 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.16 % Allowed : 12.11 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.43), residues: 452 helix: 1.51 (0.30), residues: 326 sheet: None (None), residues: 0 loop : 1.38 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.027 0.001 PHE A 22 TYR 0.013 0.001 TYR A 240 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5702 (OUTLIER) cc_final: 0.5314 (m) REVERT: A 132 SER cc_start: 0.8459 (p) cc_final: 0.8049 (m) REVERT: A 218 MET cc_start: 0.7382 (mmm) cc_final: 0.6948 (mmt) REVERT: A 346 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7498 (mtt90) REVERT: A 378 ASP cc_start: 0.7510 (m-30) cc_final: 0.7097 (m-30) REVERT: A 418 LEU cc_start: 0.8487 (tp) cc_final: 0.8114 (tp) REVERT: A 432 ILE cc_start: 0.8029 (tt) cc_final: 0.7774 (tt) REVERT: A 486 ARG cc_start: 0.5550 (mtp180) cc_final: 0.5336 (mtp180) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.1251 time to fit residues: 14.3333 Evaluate side-chains 88 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3639 Z= 0.169 Angle : 0.624 14.573 4963 Z= 0.287 Chirality : 0.038 0.138 574 Planarity : 0.004 0.048 613 Dihedral : 4.091 19.629 491 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.95 % Allowed : 13.16 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 452 helix: 1.67 (0.30), residues: 326 sheet: None (None), residues: 0 loop : 1.34 (0.66), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.017 0.001 PHE A 22 TYR 0.010 0.001 TYR A 240 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.392 Fit side-chains REVERT: A 121 CYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5345 (m) REVERT: A 132 SER cc_start: 0.8509 (p) cc_final: 0.8116 (m) REVERT: A 218 MET cc_start: 0.7444 (mmm) cc_final: 0.7207 (mmt) REVERT: A 241 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 346 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7491 (mtt90) REVERT: A 378 ASP cc_start: 0.7516 (m-30) cc_final: 0.7112 (m-30) REVERT: A 418 LEU cc_start: 0.8496 (tp) cc_final: 0.8126 (tp) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.1252 time to fit residues: 14.6017 Evaluate side-chains 91 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3639 Z= 0.169 Angle : 0.636 14.558 4963 Z= 0.292 Chirality : 0.038 0.150 574 Planarity : 0.004 0.043 613 Dihedral : 4.072 19.626 491 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.21 % Allowed : 12.89 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.43), residues: 452 helix: 1.75 (0.30), residues: 331 sheet: None (None), residues: 0 loop : 1.36 (0.67), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 22 TYR 0.011 0.001 TYR A 240 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.349 Fit side-chains REVERT: A 121 CYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5360 (m) REVERT: A 218 MET cc_start: 0.7433 (mmm) cc_final: 0.7162 (mmt) REVERT: A 227 PHE cc_start: 0.7658 (t80) cc_final: 0.7404 (t80) REVERT: A 241 GLN cc_start: 0.7266 (tm-30) cc_final: 0.7006 (tt0) REVERT: A 378 ASP cc_start: 0.7446 (m-30) cc_final: 0.7230 (m-30) REVERT: A 418 LEU cc_start: 0.8500 (tp) cc_final: 0.8140 (tp) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1163 time to fit residues: 14.3632 Evaluate side-chains 92 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.0030 chunk 43 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3639 Z= 0.167 Angle : 0.642 14.574 4963 Z= 0.294 Chirality : 0.038 0.180 574 Planarity : 0.004 0.038 613 Dihedral : 3.977 19.097 491 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.68 % Allowed : 15.79 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.43), residues: 452 helix: 1.87 (0.30), residues: 330 sheet: None (None), residues: 0 loop : 1.40 (0.65), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5324 (m) REVERT: A 218 MET cc_start: 0.7421 (mmm) cc_final: 0.7158 (mmt) REVERT: A 227 PHE cc_start: 0.7772 (t80) cc_final: 0.7488 (t80) REVERT: A 378 ASP cc_start: 0.7474 (m-30) cc_final: 0.7227 (m-30) REVERT: A 418 LEU cc_start: 0.8491 (tp) cc_final: 0.8133 (tp) REVERT: A 486 ARG cc_start: 0.7400 (mmp80) cc_final: 0.7086 (mmm160) REVERT: A 511 LEU cc_start: 0.8473 (mt) cc_final: 0.8125 (tp) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.1054 time to fit residues: 12.3889 Evaluate side-chains 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3639 Z= 0.194 Angle : 0.657 14.528 4963 Z= 0.302 Chirality : 0.039 0.194 574 Planarity : 0.004 0.037 613 Dihedral : 3.971 19.163 491 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.21 % Allowed : 16.58 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.43), residues: 452 helix: 1.86 (0.30), residues: 332 sheet: None (None), residues: 0 loop : 1.51 (0.67), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.018 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5338 (m) REVERT: A 218 MET cc_start: 0.7420 (mmm) cc_final: 0.7211 (mmt) REVERT: A 227 PHE cc_start: 0.7757 (t80) cc_final: 0.7521 (t80) REVERT: A 378 ASP cc_start: 0.7461 (m-30) cc_final: 0.7208 (m-30) REVERT: A 447 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7855 (tm-30) REVERT: A 448 MET cc_start: 0.8636 (mmm) cc_final: 0.8203 (mmm) outliers start: 16 outliers final: 14 residues processed: 85 average time/residue: 0.1013 time to fit residues: 11.5858 Evaluate side-chains 88 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3639 Z= 0.175 Angle : 0.663 14.559 4963 Z= 0.301 Chirality : 0.039 0.216 574 Planarity : 0.004 0.035 613 Dihedral : 3.963 18.937 491 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.21 % Allowed : 16.84 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.43), residues: 452 helix: 1.84 (0.30), residues: 332 sheet: None (None), residues: 0 loop : 1.38 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5347 (m) REVERT: A 218 MET cc_start: 0.7489 (mmm) cc_final: 0.7280 (mmt) REVERT: A 378 ASP cc_start: 0.7488 (m-30) cc_final: 0.7268 (m-30) REVERT: A 447 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7809 (tm-30) REVERT: A 448 MET cc_start: 0.8664 (mmm) cc_final: 0.8215 (mmm) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.1052 time to fit residues: 11.6371 Evaluate side-chains 81 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3639 Z= 0.206 Angle : 0.703 14.521 4963 Z= 0.315 Chirality : 0.040 0.222 574 Planarity : 0.004 0.037 613 Dihedral : 4.024 19.078 491 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.21 % Allowed : 17.63 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.42), residues: 452 helix: 1.78 (0.30), residues: 332 sheet: None (None), residues: 0 loop : 1.36 (0.67), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.019 0.001 PHE A 22 TYR 0.013 0.001 TYR A 352 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5386 (m) REVERT: A 378 ASP cc_start: 0.7448 (m-30) cc_final: 0.7205 (m-30) outliers start: 16 outliers final: 14 residues processed: 82 average time/residue: 0.1028 time to fit residues: 11.3533 Evaluate side-chains 86 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3639 Z= 0.186 Angle : 0.730 14.564 4963 Z= 0.324 Chirality : 0.041 0.239 574 Planarity : 0.004 0.034 613 Dihedral : 3.997 18.479 491 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.68 % Allowed : 17.89 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.43), residues: 452 helix: 1.80 (0.30), residues: 333 sheet: None (None), residues: 0 loop : 1.39 (0.68), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.022 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.004 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5356 (m) REVERT: A 378 ASP cc_start: 0.7490 (m-30) cc_final: 0.7268 (m-30) outliers start: 14 outliers final: 11 residues processed: 83 average time/residue: 0.1053 time to fit residues: 11.7076 Evaluate side-chains 83 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.156116 restraints weight = 4582.206| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.70 r_work: 0.3719 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3639 Z= 0.169 Angle : 0.729 14.595 4963 Z= 0.320 Chirality : 0.041 0.244 574 Planarity : 0.004 0.031 613 Dihedral : 3.975 18.281 491 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.68 % Allowed : 18.68 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.42), residues: 452 helix: 1.89 (0.30), residues: 325 sheet: None (None), residues: 0 loop : 1.33 (0.66), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.021 0.001 PHE A 22 TYR 0.007 0.001 TYR A 352 ARG 0.003 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.91 seconds wall clock time: 23 minutes 21.75 seconds (1401.75 seconds total)