Starting phenix.real_space_refine on Tue Mar 11 14:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2025/7t4l_25679.cif" } resolution = 3.28 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= 0.009 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 3873 2.51 5 N 1022 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6062 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3042 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3020 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 5.37, per 1000 atoms: 0.89 Number of scatterers: 6062 At special positions: 0 Unit cell: (116.22, 77.22, 75.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1125 8.00 N 1022 7.00 C 3873 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 - 3.00 Amino acid : True - 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: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 45.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.678A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.883A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.807A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.610A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.292A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.778A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.478A pdb=" N CYS B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 361 " --> pdb=" O PHE B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 361' Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.692A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.523A pdb=" N ASP B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.827A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.790A pdb=" N ARG B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.524A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.895A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 166 removed outlier: 5.456A pdb=" N LEU B 161 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 177 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 163 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 175 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N SER B 251 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR B 221 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 253 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 372 279 hydrogen bonds defined for protein. 807 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: 1.92 Time building geometry restraints manager: 1.80 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: 1845 1.34 - 1.46: 1246 1.46 - 1.58: 3020 1.58 - 1.70: 8 1.70 - 1.83: 63 Bond restraints: 6182 Sorted by residual: bond pdb=" C VAL B 216 " pdb=" N PRO B 217 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.76e+00 bond pdb=" C LEU A 543 " pdb=" N PRO A 544 " ideal model delta sigma weight residual 1.334 1.362 -0.028 1.51e-02 4.39e+03 3.50e+00 bond pdb=" CB VAL A 354 " pdb=" CG1 VAL A 354 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C LEU B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.334 1.358 -0.024 1.51e-02 4.39e+03 2.55e+00 bond pdb=" CB PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 1.492 1.415 0.077 5.00e-02 4.00e+02 2.35e+00 ... (remaining 6177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 8291 3.70 - 7.40: 73 7.40 - 11.10: 4 11.10 - 14.80: 1 14.80 - 18.50: 1 Bond angle restraints: 8370 Sorted by residual: angle pdb=" C GLU A 163 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 125.00 106.50 18.50 4.10e+00 5.95e-02 2.04e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 130.79 -14.49 3.50e+00 8.16e-02 1.71e+01 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.37e+01 angle pdb=" N MET B 211 " pdb=" CA MET B 211 " pdb=" CB MET B 211 " ideal model delta sigma weight residual 110.07 115.32 -5.25 1.45e+00 4.76e-01 1.31e+01 angle pdb=" CB GLU B 570 " pdb=" CG GLU B 570 " pdb=" CD GLU B 570 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 ... (remaining 8365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 3371 15.87 - 31.74: 312 31.74 - 47.61: 74 47.61 - 63.48: 17 63.48 - 79.35: 6 Dihedral angle restraints: 3780 sinusoidal: 1540 harmonic: 2240 Sorted by residual: dihedral pdb=" C VAL B 216 " pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" CB VAL B 216 " ideal model delta harmonic sigma weight residual -122.00 -130.37 8.37 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" N SEP A 202 " pdb=" CA SEP A 202 " pdb=" CB SEP A 202 " pdb=" OG SEP A 202 " ideal model delta sinusoidal sigma weight residual -60.00 -5.69 -54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CG ARG B 469 " pdb=" CD ARG B 469 " pdb=" NE ARG B 469 " pdb=" CZ ARG B 469 " ideal model delta sinusoidal sigma weight residual 180.00 139.20 40.80 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 3777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 630 0.044 - 0.088: 214 0.088 - 0.132: 80 0.132 - 0.176: 18 0.176 - 0.220: 5 Chirality restraints: 947 Sorted by residual: chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL B 216 " pdb=" N VAL B 216 " pdb=" C VAL B 216 " pdb=" CB VAL B 216 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 944 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 163 " -0.122 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 164 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.109 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 395 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO B 396 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.020 2.00e-02 2.50e+03 1.74e-02 6.07e+00 pdb=" CG TYR A 373 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.003 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1289 2.80 - 3.32: 5680 3.32 - 3.85: 9785 3.85 - 4.37: 11492 4.37 - 4.90: 19820 Nonbonded interactions: 48066 Sorted by model distance: nonbonded pdb=" O THR A 215 " pdb=" OH TYR A 221 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP B 428 " pdb=" OG1 THR B 430 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 438 " pdb=" O LEU A 462 " model vdw 2.315 3.040 nonbonded pdb=" O TYR A 198 " pdb=" OG SER A 204 " model vdw 2.334 3.040 nonbonded pdb=" OH TYR B 438 " pdb=" O LEU B 462 " model vdw 2.345 3.040 ... (remaining 48061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 178 or (resid 179 and (name N or name CA or name C or n \ ame O or name CB )) or resid 188 through 223 or resid 236 through 256 or resid 2 \ 85 through 493 or (resid 494 and (name N or name CA or name C or name O or name \ CB )) or resid 495 through 574)) selection = (chain 'B' and (resid 120 through 136 or resid 148 through 256 or resid 285 thro \ ugh 511 or resid 541 through 574)) } 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: 4.010 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.780 Find NCS groups from input model: 0.240 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.005 0.077 6182 Z= 0.318 Angle : 0.948 18.498 8370 Z= 0.506 Chirality : 0.053 0.220 947 Planarity : 0.009 0.185 1056 Dihedral : 13.459 79.353 2314 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 1.35 (0.30), residues: 725 helix: 2.77 (0.30), residues: 303 sheet: -0.42 (0.46), residues: 111 loop : -0.49 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 505 HIS 0.007 0.002 HIS A 243 PHE 0.023 0.003 PHE B 399 TYR 0.043 0.003 TYR A 373 ARG 0.007 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.718 Fit side-chains REVERT: A 377 ASP cc_start: 0.8323 (m-30) cc_final: 0.8042 (t0) REVERT: A 504 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 350 TYR cc_start: 0.7914 (m-80) cc_final: 0.7621 (m-10) REVERT: B 547 GLU cc_start: 0.7717 (tp30) cc_final: 0.7476 (mt-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1476 time to fit residues: 21.6638 Evaluate side-chains 75 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 326 ASN B 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120079 restraints weight = 8254.250| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.77 r_work: 0.3269 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6182 Z= 0.147 Angle : 0.522 6.871 8370 Z= 0.268 Chirality : 0.039 0.169 947 Planarity : 0.005 0.100 1056 Dihedral : 5.284 82.747 818 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.45 % Allowed : 7.46 % Favored : 92.09 % 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: 1.77 (0.31), residues: 725 helix: 2.82 (0.29), residues: 309 sheet: -0.26 (0.46), residues: 110 loop : 0.05 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 505 HIS 0.003 0.001 HIS A 243 PHE 0.017 0.001 PHE A 253 TYR 0.014 0.001 TYR B 300 ARG 0.002 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.710 Fit side-chains REVERT: A 377 ASP cc_start: 0.8500 (m-30) cc_final: 0.8050 (t0) REVERT: A 473 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: B 376 GLU cc_start: 0.7442 (mp0) cc_final: 0.6933 (mp0) REVERT: B 547 GLU cc_start: 0.8048 (tp30) cc_final: 0.7715 (mt-10) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.1613 time to fit residues: 20.6056 Evaluate side-chains 83 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111948 restraints weight = 8309.891| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.78 r_work: 0.3149 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6182 Z= 0.301 Angle : 0.557 7.109 8370 Z= 0.285 Chirality : 0.042 0.170 947 Planarity : 0.005 0.070 1056 Dihedral : 5.165 83.989 818 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.94 % Allowed : 8.36 % Favored : 89.70 % 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: 1.62 (0.30), residues: 725 helix: 2.54 (0.28), residues: 310 sheet: -0.29 (0.45), residues: 112 loop : 0.15 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 505 HIS 0.005 0.001 HIS A 559 PHE 0.016 0.002 PHE B 452 TYR 0.022 0.002 TYR A 373 ARG 0.004 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.656 Fit side-chains REVERT: A 377 ASP cc_start: 0.8541 (m-30) cc_final: 0.7989 (t0) REVERT: B 213 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6224 (ttp80) REVERT: B 547 GLU cc_start: 0.8110 (tp30) cc_final: 0.7792 (mt-10) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1440 time to fit residues: 17.7369 Evaluate side-chains 80 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 572 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113376 restraints weight = 8527.210| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.75 r_work: 0.3193 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6182 Z= 0.247 Angle : 0.514 7.054 8370 Z= 0.263 Chirality : 0.041 0.158 947 Planarity : 0.004 0.055 1056 Dihedral : 5.056 83.525 818 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.49 % Allowed : 8.06 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 725 helix: 2.59 (0.28), residues: 310 sheet: -0.33 (0.46), residues: 105 loop : 0.13 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.003 0.001 HIS A 559 PHE 0.013 0.001 PHE B 452 TYR 0.015 0.001 TYR A 494 ARG 0.002 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.644 Fit side-chains REVERT: A 377 ASP cc_start: 0.8450 (m-30) cc_final: 0.8067 (t0) REVERT: A 383 ASN cc_start: 0.8385 (m110) cc_final: 0.7664 (p0) REVERT: B 213 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6556 (ttp80) REVERT: B 376 GLU cc_start: 0.7562 (mp0) cc_final: 0.7333 (mp0) REVERT: B 547 GLU cc_start: 0.8088 (tp30) cc_final: 0.7873 (mt-10) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.1473 time to fit residues: 18.0229 Evaluate side-chains 84 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112989 restraints weight = 8468.909| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.75 r_work: 0.3172 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6182 Z= 0.236 Angle : 0.504 7.075 8370 Z= 0.256 Chirality : 0.040 0.165 947 Planarity : 0.004 0.046 1056 Dihedral : 4.985 82.872 818 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 8.36 % Favored : 90.00 % 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: 1.69 (0.30), residues: 725 helix: 2.62 (0.28), residues: 310 sheet: -0.33 (0.46), residues: 105 loop : 0.16 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.003 0.001 HIS A 559 PHE 0.012 0.001 PHE B 452 TYR 0.017 0.001 TYR A 494 ARG 0.002 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.663 Fit side-chains REVERT: A 377 ASP cc_start: 0.8451 (m-30) cc_final: 0.8149 (m-30) REVERT: A 383 ASN cc_start: 0.8430 (m110) cc_final: 0.7758 (p0) REVERT: A 504 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 213 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6544 (ttp80) REVERT: B 547 GLU cc_start: 0.8068 (tp30) cc_final: 0.7843 (mt-10) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1551 time to fit residues: 18.1029 Evaluate side-chains 85 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 572 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114885 restraints weight = 8270.595| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.62 r_work: 0.3185 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6182 Z= 0.215 Angle : 0.507 8.074 8370 Z= 0.255 Chirality : 0.040 0.163 947 Planarity : 0.004 0.041 1056 Dihedral : 4.946 82.246 818 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.24 % Allowed : 8.81 % Favored : 88.96 % 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: 1.75 (0.31), residues: 725 helix: 2.70 (0.28), residues: 310 sheet: -0.31 (0.47), residues: 105 loop : 0.18 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.011 0.001 PHE B 452 TYR 0.018 0.001 TYR A 494 ARG 0.002 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.644 Fit side-chains REVERT: A 377 ASP cc_start: 0.8412 (m-30) cc_final: 0.8170 (m-30) REVERT: A 383 ASN cc_start: 0.8400 (m110) cc_final: 0.7760 (p0) REVERT: A 390 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: B 547 GLU cc_start: 0.8061 (tp30) cc_final: 0.7831 (mt-10) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.1462 time to fit residues: 17.5257 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 73 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 0.0770 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114130 restraints weight = 8376.525| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.77 r_work: 0.3190 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6182 Z= 0.180 Angle : 0.487 7.039 8370 Z= 0.247 Chirality : 0.039 0.161 947 Planarity : 0.004 0.040 1056 Dihedral : 4.866 81.539 818 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.24 % Allowed : 8.96 % Favored : 88.81 % 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: 1.86 (0.31), residues: 725 helix: 2.80 (0.28), residues: 310 sheet: -0.21 (0.48), residues: 105 loop : 0.19 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.003 0.001 HIS B 332 PHE 0.010 0.001 PHE B 452 TYR 0.020 0.001 TYR A 494 ARG 0.002 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.647 Fit side-chains REVERT: A 377 ASP cc_start: 0.8379 (m-30) cc_final: 0.8176 (m-30) REVERT: A 383 ASN cc_start: 0.8359 (m110) cc_final: 0.7749 (p0) REVERT: A 390 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: A 504 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 547 GLU cc_start: 0.8039 (tp30) cc_final: 0.7822 (mt-10) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.1355 time to fit residues: 16.0003 Evaluate side-chains 86 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113811 restraints weight = 8365.900| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.62 r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6182 Z= 0.273 Angle : 0.533 9.625 8370 Z= 0.267 Chirality : 0.040 0.156 947 Planarity : 0.004 0.040 1056 Dihedral : 4.895 80.961 818 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.24 % Allowed : 9.55 % Favored : 88.21 % 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: 1.74 (0.31), residues: 725 helix: 2.67 (0.28), residues: 310 sheet: -0.28 (0.48), residues: 105 loop : 0.18 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 PHE 0.012 0.001 PHE B 452 TYR 0.020 0.001 TYR A 494 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.662 Fit side-chains REVERT: A 377 ASP cc_start: 0.8447 (m-30) cc_final: 0.8206 (m-30) REVERT: A 383 ASN cc_start: 0.8398 (m110) cc_final: 0.7826 (p0) REVERT: A 390 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: A 504 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 376 GLU cc_start: 0.7688 (mp0) cc_final: 0.7433 (mp0) REVERT: B 547 GLU cc_start: 0.8067 (tp30) cc_final: 0.7815 (mt-10) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.1396 time to fit residues: 16.6139 Evaluate side-chains 87 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 38 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: B 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113360 restraints weight = 8419.067| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.62 r_work: 0.3182 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6182 Z= 0.283 Angle : 0.549 9.298 8370 Z= 0.276 Chirality : 0.041 0.164 947 Planarity : 0.004 0.041 1056 Dihedral : 4.897 79.791 818 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.24 % Allowed : 10.15 % Favored : 87.61 % 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: 1.64 (0.31), residues: 725 helix: 2.55 (0.28), residues: 310 sheet: -0.32 (0.49), residues: 105 loop : 0.15 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 PHE 0.011 0.001 PHE B 452 TYR 0.019 0.001 TYR A 494 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 390 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: B 376 GLU cc_start: 0.7583 (mp0) cc_final: 0.7305 (mp0) REVERT: B 547 GLU cc_start: 0.8071 (tp30) cc_final: 0.7861 (mt-10) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1392 time to fit residues: 16.6288 Evaluate side-chains 87 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110355 restraints weight = 8542.037| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.78 r_work: 0.3161 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6182 Z= 0.295 Angle : 0.564 9.008 8370 Z= 0.284 Chirality : 0.041 0.171 947 Planarity : 0.004 0.042 1056 Dihedral : 4.901 79.483 818 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 10.60 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.31), residues: 725 helix: 2.48 (0.28), residues: 310 sheet: -0.40 (0.49), residues: 105 loop : 0.18 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 129 HIS 0.004 0.001 HIS A 559 PHE 0.013 0.001 PHE B 452 TYR 0.020 0.002 TYR A 494 ARG 0.002 0.000 ARG A 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 390 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: B 376 GLU cc_start: 0.7608 (mp0) cc_final: 0.7329 (mp0) REVERT: B 547 GLU cc_start: 0.8110 (tp30) cc_final: 0.7898 (mt-10) outliers start: 16 outliers final: 15 residues processed: 82 average time/residue: 0.1413 time to fit residues: 16.8034 Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110377 restraints weight = 8535.923| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.69 r_work: 0.3148 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6182 Z= 0.302 Angle : 0.575 8.962 8370 Z= 0.290 Chirality : 0.041 0.172 947 Planarity : 0.004 0.042 1056 Dihedral : 4.919 79.337 818 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.24 % Allowed : 11.04 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.31), residues: 725 helix: 2.46 (0.29), residues: 310 sheet: -0.25 (0.50), residues: 95 loop : 0.02 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 PHE 0.012 0.001 PHE B 452 TYR 0.020 0.002 TYR A 494 ARG 0.001 0.000 ARG A 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.47 seconds wall clock time: 51 minutes 39.30 seconds (3099.30 seconds total)