Starting phenix.real_space_refine on Tue Mar 3 14:30:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4l_25679/03_2026/7t4l_25679.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4l_25679/03_2026/7t4l_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_2026/7t4l_25679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2026/7t4l_25679.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2026/7t4l_25679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4l_25679/03_2026/7t4l_25679.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'TYR: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: 1.29, per 1000 atoms: 0.21 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: 0.38 Conformation dependent library (CDL) restraints added in 304.4 milliseconds 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: 0.15 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: 0.96 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 7.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- 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= 0.220 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG B 455 TYR 0.043 0.003 TYR A 373 PHE 0.023 0.003 PHE B 399 TRP 0.022 0.002 TRP A 505 HIS 0.007 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6182) covalent geometry : angle 0.94792 ( 8370) hydrogen bonds : bond 0.13801 ( 279) hydrogen bonds : angle 5.42248 ( 807) *********************** 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 : 0.184 Fit side-chains REVERT: A 377 ASP cc_start: 0.8323 (m-30) cc_final: 0.8041 (t0) REVERT: A 504 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8019 (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: 0.0524 time to fit residues: 7.7747 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 B 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117029 restraints weight = 8340.981| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.78 r_work: 0.3224 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6182 Z= 0.133 Angle : 0.541 6.938 8370 Z= 0.277 Chirality : 0.040 0.171 947 Planarity : 0.005 0.101 1056 Dihedral : 5.309 82.696 818 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.90 % Allowed : 7.16 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.31), residues: 725 helix: 2.81 (0.29), residues: 307 sheet: -0.30 (0.46), residues: 110 loop : -0.00 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 455 TYR 0.016 0.001 TYR B 300 PHE 0.018 0.002 PHE A 253 TRP 0.011 0.001 TRP A 505 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6182) covalent geometry : angle 0.54082 ( 8370) hydrogen bonds : bond 0.04627 ( 279) hydrogen bonds : angle 4.59760 ( 807) *********************** 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 92 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 377 ASP cc_start: 0.8524 (m-30) cc_final: 0.8035 (t0) REVERT: B 376 GLU cc_start: 0.7454 (mp0) cc_final: 0.6961 (mp0) REVERT: B 547 GLU cc_start: 0.8067 (tp30) cc_final: 0.7720 (mt-10) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.0717 time to fit residues: 8.8551 Evaluate side-chains 80 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 195 MET 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 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 378 GLN B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111206 restraints weight = 8275.874| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.77 r_work: 0.3137 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6182 Z= 0.199 Angle : 0.558 7.083 8370 Z= 0.283 Chirality : 0.042 0.168 947 Planarity : 0.005 0.069 1056 Dihedral : 5.183 83.769 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 7.91 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 725 helix: 2.54 (0.28), residues: 309 sheet: -0.32 (0.46), residues: 105 loop : 0.15 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 464 TYR 0.023 0.002 TYR A 373 PHE 0.016 0.002 PHE B 452 TRP 0.012 0.001 TRP A 505 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6182) covalent geometry : angle 0.55795 ( 8370) hydrogen bonds : bond 0.04744 ( 279) hydrogen bonds : angle 4.47551 ( 807) *********************** 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 96 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.236 Fit side-chains REVERT: A 377 ASP cc_start: 0.8551 (m-30) cc_final: 0.7988 (t0) REVERT: A 383 ASN cc_start: 0.8216 (m110) cc_final: 0.7358 (p0) REVERT: B 213 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6253 (ttp80) REVERT: B 440 GLU cc_start: 0.7635 (mp0) cc_final: 0.7349 (mp0) REVERT: B 547 GLU cc_start: 0.8119 (tp30) cc_final: 0.7800 (mt-10) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.0664 time to fit residues: 8.3028 Evaluate side-chains 83 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 343 ASP 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 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 378 GLN A 572 HIS B 189 GLN B 378 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112678 restraints weight = 8479.294| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.74 r_work: 0.3175 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2102 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= 0.151 Angle : 0.512 7.048 8370 Z= 0.261 Chirality : 0.040 0.162 947 Planarity : 0.004 0.054 1056 Dihedral : 5.072 83.213 818 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.64 % Allowed : 9.10 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 725 helix: 2.55 (0.28), residues: 310 sheet: -0.38 (0.46), residues: 105 loop : 0.15 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 239 TYR 0.015 0.001 TYR A 373 PHE 0.012 0.001 PHE A 253 TRP 0.008 0.001 TRP A 505 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6182) covalent geometry : angle 0.51248 ( 8370) hydrogen bonds : bond 0.04203 ( 279) hydrogen bonds : angle 4.31106 ( 807) *********************** 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 93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.221 Fit side-chains REVERT: A 377 ASP cc_start: 0.8477 (m-30) cc_final: 0.8140 (m-30) REVERT: A 383 ASN cc_start: 0.8415 (m110) cc_final: 0.7699 (p0) REVERT: B 213 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6623 (ttp80) REVERT: B 440 GLU cc_start: 0.7515 (mp0) cc_final: 0.7206 (mp0) REVERT: B 547 GLU cc_start: 0.8078 (tp30) cc_final: 0.7852 (mt-10) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.0666 time to fit residues: 8.2935 Evaluate side-chains 85 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 343 ASP 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 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 73 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 378 GLN B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113807 restraints weight = 8506.831| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.78 r_work: 0.3202 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6182 Z= 0.132 Angle : 0.503 7.543 8370 Z= 0.253 Chirality : 0.039 0.160 947 Planarity : 0.004 0.045 1056 Dihedral : 4.979 82.663 818 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.09 % Allowed : 8.51 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.30), residues: 725 helix: 2.64 (0.28), residues: 310 sheet: -0.32 (0.46), residues: 105 loop : 0.17 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.012 0.001 TYR B 546 PHE 0.011 0.001 PHE A 253 TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6182) covalent geometry : angle 0.50295 ( 8370) hydrogen bonds : bond 0.03865 ( 279) hydrogen bonds : angle 4.16646 ( 807) *********************** 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: 14 poor density : 77 time to evaluate : 0.244 Fit side-chains REVERT: A 377 ASP cc_start: 0.8423 (m-30) cc_final: 0.8142 (m-30) REVERT: A 383 ASN cc_start: 0.8423 (m110) cc_final: 0.7769 (p0) REVERT: A 390 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: A 504 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 213 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6679 (ttp80) REVERT: B 440 GLU cc_start: 0.7506 (mp0) cc_final: 0.7200 (mp0) REVERT: B 547 GLU cc_start: 0.8051 (tp30) cc_final: 0.7841 (mt-10) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.0648 time to fit residues: 7.6481 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 : 0.197 ------------------------------------------------------------------------------- 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 343 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 572 HIS B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114706 restraints weight = 8433.790| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.79 r_work: 0.3212 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2375 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= 0.110 Angle : 0.483 7.219 8370 Z= 0.243 Chirality : 0.039 0.161 947 Planarity : 0.004 0.040 1056 Dihedral : 4.865 82.041 818 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.09 % Allowed : 9.40 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.31), residues: 725 helix: 2.71 (0.28), residues: 312 sheet: -0.15 (0.47), residues: 105 loop : 0.23 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 239 TYR 0.011 0.001 TYR B 546 PHE 0.011 0.001 PHE A 253 TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6182) covalent geometry : angle 0.48276 ( 8370) hydrogen bonds : bond 0.03480 ( 279) hydrogen bonds : angle 4.06337 ( 807) *********************** 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 90 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.286 Fit side-chains REVERT: A 377 ASP cc_start: 0.8407 (m-30) cc_final: 0.8177 (m-30) REVERT: A 383 ASN cc_start: 0.8353 (m110) cc_final: 0.7729 (p0) REVERT: A 390 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: B 213 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6916 (mtm-85) REVERT: B 376 GLU cc_start: 0.7628 (mp0) cc_final: 0.7384 (mp0) REVERT: B 547 GLU cc_start: 0.8059 (tp30) cc_final: 0.7855 (mt-10) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.0672 time to fit residues: 7.9265 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 : 0.249 ------------------------------------------------------------------------------- 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 343 ASP 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 213 ARG 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 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.0030 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111757 restraints weight = 8540.839| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.77 r_work: 0.3164 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6182 Z= 0.144 Angle : 0.498 7.046 8370 Z= 0.251 Chirality : 0.040 0.159 947 Planarity : 0.004 0.034 1056 Dihedral : 4.854 81.472 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 10.30 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.31), residues: 725 helix: 2.70 (0.28), residues: 310 sheet: -0.16 (0.48), residues: 105 loop : 0.19 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 455 TYR 0.012 0.001 TYR A 373 PHE 0.012 0.001 PHE B 452 TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6182) covalent geometry : angle 0.49805 ( 8370) hydrogen bonds : bond 0.03841 ( 279) hydrogen bonds : angle 4.09514 ( 807) *********************** 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 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.243 Fit side-chains REVERT: A 377 ASP cc_start: 0.8478 (m-30) cc_final: 0.8242 (m-30) REVERT: A 383 ASN cc_start: 0.8401 (m110) cc_final: 0.7776 (p0) REVERT: A 390 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: A 504 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 376 GLU cc_start: 0.7619 (mp0) cc_final: 0.7399 (mp0) REVERT: B 440 GLU cc_start: 0.7464 (mp0) cc_final: 0.7158 (mp0) REVERT: B 547 GLU cc_start: 0.8094 (tp30) cc_final: 0.7874 (mt-10) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.0628 time to fit residues: 7.9169 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 343 ASP 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 216 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 572 HIS B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112957 restraints weight = 8451.699| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.73 r_work: 0.3181 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6182 Z= 0.120 Angle : 0.488 6.966 8370 Z= 0.246 Chirality : 0.039 0.175 947 Planarity : 0.003 0.034 1056 Dihedral : 4.812 80.828 818 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.69 % Allowed : 9.85 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.31), residues: 725 helix: 2.69 (0.28), residues: 312 sheet: -0.17 (0.48), residues: 105 loop : 0.24 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 213 TYR 0.020 0.001 TYR A 494 PHE 0.010 0.001 PHE B 452 TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6182) covalent geometry : angle 0.48846 ( 8370) hydrogen bonds : bond 0.03576 ( 279) hydrogen bonds : angle 4.03298 ( 807) *********************** 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 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.300 Fit side-chains REVERT: A 377 ASP cc_start: 0.8462 (m-30) cc_final: 0.8239 (m-30) REVERT: A 383 ASN cc_start: 0.8368 (m110) cc_final: 0.7734 (p0) REVERT: A 390 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: A 504 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8043 (tm-30) REVERT: B 376 GLU cc_start: 0.7601 (mp0) cc_final: 0.7375 (mp0) REVERT: B 440 GLU cc_start: 0.7460 (mp0) cc_final: 0.7146 (mp0) REVERT: B 547 GLU cc_start: 0.8062 (tp30) cc_final: 0.7852 (mt-10) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.0626 time to fit residues: 7.8295 Evaluate side-chains 92 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 195 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112831 restraints weight = 8473.352| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.63 r_work: 0.3173 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6182 Z= 0.192 Angle : 0.543 7.024 8370 Z= 0.274 Chirality : 0.041 0.169 947 Planarity : 0.004 0.035 1056 Dihedral : 4.893 79.970 818 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 10.15 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.31), residues: 725 helix: 2.58 (0.28), residues: 310 sheet: -0.30 (0.48), residues: 105 loop : 0.21 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.020 0.002 TYR A 494 PHE 0.012 0.001 PHE B 452 TRP 0.009 0.001 TRP A 129 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 6182) covalent geometry : angle 0.54274 ( 8370) hydrogen bonds : bond 0.04406 ( 279) hydrogen bonds : angle 4.22057 ( 807) *********************** 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 92 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.242 Fit side-chains REVERT: A 377 ASP cc_start: 0.8425 (m-30) cc_final: 0.8206 (m-30) REVERT: A 390 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: A 504 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 376 GLU cc_start: 0.7606 (mp0) cc_final: 0.7369 (mp0) REVERT: B 547 GLU cc_start: 0.8076 (tp30) cc_final: 0.7849 (mt-10) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.0638 time to fit residues: 7.6933 Evaluate side-chains 86 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 216 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 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 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 378 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 = 0.140829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110735 restraints weight = 8441.624| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.64 r_work: 0.3159 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2905 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= 0.184 Angle : 0.547 7.077 8370 Z= 0.277 Chirality : 0.041 0.172 947 Planarity : 0.004 0.035 1056 Dihedral : 4.889 79.626 818 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.24 % Allowed : 10.30 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.31), residues: 725 helix: 2.51 (0.29), residues: 310 sheet: -0.32 (0.48), residues: 105 loop : 0.20 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.021 0.002 TYR A 494 PHE 0.012 0.001 PHE B 452 TRP 0.009 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6182) covalent geometry : angle 0.54650 ( 8370) hydrogen bonds : bond 0.04265 ( 279) hydrogen bonds : angle 4.21600 ( 807) ********************** 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 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.196 Fit side-chains REVERT: A 377 ASP cc_start: 0.8527 (m-30) cc_final: 0.8290 (m-30) REVERT: A 390 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: A 504 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 376 GLU cc_start: 0.7627 (mp0) cc_final: 0.7374 (mp0) REVERT: B 547 GLU cc_start: 0.8091 (tp30) cc_final: 0.7820 (mt-10) outliers start: 15 outliers final: 14 residues processed: 82 average time/residue: 0.0616 time to fit residues: 7.3565 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 216 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 35 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 49 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 B 326 ASN B 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112972 restraints weight = 8387.188| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.73 r_work: 0.3202 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6182 Z= 0.116 Angle : 0.517 6.925 8370 Z= 0.263 Chirality : 0.039 0.170 947 Planarity : 0.003 0.035 1056 Dihedral : 4.786 79.240 818 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.94 % Allowed : 10.60 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.31), residues: 725 helix: 2.72 (0.28), residues: 310 sheet: -0.22 (0.49), residues: 105 loop : 0.22 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 239 TYR 0.021 0.001 TYR A 494 PHE 0.010 0.001 PHE B 452 TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6182) covalent geometry : angle 0.51743 ( 8370) hydrogen bonds : bond 0.03534 ( 279) hydrogen bonds : angle 4.06180 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.29 seconds wall clock time: 25 minutes 35.32 seconds (1535.32 seconds total)