Starting phenix.real_space_refine on Fri Dec 27 17:12:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4l_25679/12_2024/7t4l_25679.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4l_25679/12_2024/7t4l_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_25679/12_2024/7t4l_25679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4l_25679/12_2024/7t4l_25679.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4l_25679/12_2024/7t4l_25679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4l_25679/12_2024/7t4l_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-5532/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: 5.54, per 1000 atoms: 0.91 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: 1.46 Conformation dependent library (CDL) restraints added in 881.0 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: 0.63 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: 1.61 Time building geometry restraints manager: 1.69 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: 5.710 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.220 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- 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 : 0.705 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: 0.1455 time to fit residues: 21.4202 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 : 0.673 ------------------------------------------------------------------------------- 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: 0.0770 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.1138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6182 Z= 0.147 Angle : 0.516 6.860 8370 Z= 0.265 Chirality : 0.039 0.172 947 Planarity : 0.005 0.099 1056 Dihedral : 5.275 82.966 818 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.60 % Allowed : 7.46 % 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 (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: 1.79 (0.31), residues: 725 helix: 2.82 (0.29), residues: 309 sheet: -0.24 (0.46), residues: 110 loop : 0.07 (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 0.015 0.001 TYR B 300 ARG 0.002 0.000 ARG B 239 *********************** 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 97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.745 Fit side-chains REVERT: A 377 ASP cc_start: 0.8256 (m-30) cc_final: 0.8034 (t0) REVERT: B 376 GLU cc_start: 0.7108 (mp0) cc_final: 0.6652 (mp0) outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 0.1577 time to fit residues: 20.6641 Evaluate side-chains 82 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LEU 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 37 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6182 Z= 0.295 Angle : 0.553 7.081 8370 Z= 0.282 Chirality : 0.042 0.159 947 Planarity : 0.005 0.068 1056 Dihedral : 5.135 84.115 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.94 % Allowed : 8.81 % 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 (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: 1.63 (0.30), residues: 725 helix: 2.54 (0.28), residues: 310 sheet: -0.25 (0.45), residues: 112 loop : 0.13 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.003 0.000 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 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.689 Fit side-chains REVERT: A 377 ASP cc_start: 0.8333 (m-30) cc_final: 0.7983 (t0) REVERT: B 213 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6469 (ttp80) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1517 time to fit residues: 17.8336 Evaluate side-chains 79 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.3980 chunk 71 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6182 Z= 0.172 Angle : 0.486 6.887 8370 Z= 0.249 Chirality : 0.039 0.156 947 Planarity : 0.004 0.053 1056 Dihedral : 4.996 83.678 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.34 % Allowed : 8.96 % 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: 1.78 (0.30), residues: 725 helix: 2.73 (0.28), residues: 310 sheet: -0.22 (0.46), residues: 105 loop : 0.14 (0.34), 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 0.012 0.001 PHE A 253 TYR 0.017 0.001 TYR A 494 ARG 0.002 0.000 ARG B 239 *********************** 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 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.714 Fit side-chains REVERT: A 377 ASP cc_start: 0.8287 (m-30) cc_final: 0.8011 (t0) REVERT: A 504 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 213 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6453 (ttp80) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1519 time to fit residues: 17.5790 Evaluate side-chains 82 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 A residue 558 LEU 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 59 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 18 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 378 GLN B 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6182 Z= 0.298 Angle : 0.538 7.136 8370 Z= 0.273 Chirality : 0.041 0.156 947 Planarity : 0.004 0.044 1056 Dihedral : 5.061 83.137 818 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.24 % Allowed : 8.06 % 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: 1.63 (0.30), residues: 725 helix: 2.53 (0.28), residues: 310 sheet: -0.32 (0.45), residues: 105 loop : 0.16 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.004 0.001 HIS A 559 PHE 0.014 0.001 PHE B 452 TYR 0.019 0.002 TYR A 373 ARG 0.003 0.000 ARG B 455 *********************** 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 97 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.680 Fit side-chains REVERT: A 377 ASP cc_start: 0.8317 (m-30) cc_final: 0.8029 (m-30) REVERT: A 383 ASN cc_start: 0.8330 (m110) cc_final: 0.7762 (p0) REVERT: A 504 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 213 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6463 (ttp80) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.1606 time to fit residues: 19.6973 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 A residue 433 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 156 LEU 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: 0.9990 chunk 64 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2455 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= 0.191 Angle : 0.496 7.040 8370 Z= 0.250 Chirality : 0.040 0.177 947 Planarity : 0.004 0.040 1056 Dihedral : 4.936 82.361 818 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.09 % Allowed : 9.25 % Favored : 88.66 % 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: 1.78 (0.31), residues: 725 helix: 2.69 (0.28), residues: 310 sheet: -0.23 (0.46), residues: 105 loop : 0.20 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS B 332 PHE 0.011 0.001 PHE B 452 TYR 0.018 0.001 TYR A 494 ARG 0.003 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 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.719 Fit side-chains REVERT: A 377 ASP cc_start: 0.8263 (m-30) cc_final: 0.8061 (m-30) REVERT: A 383 ASN cc_start: 0.8273 (m110) cc_final: 0.7724 (p0) REVERT: A 390 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: B 213 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6743 (mtm-85) REVERT: B 376 GLU cc_start: 0.7342 (mp0) cc_final: 0.7116 (mp0) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.1559 time to fit residues: 18.2212 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 LEU 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 69 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6182 Z= 0.267 Angle : 0.530 8.913 8370 Z= 0.266 Chirality : 0.040 0.163 947 Planarity : 0.004 0.039 1056 Dihedral : 4.929 81.627 818 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.54 % Allowed : 9.55 % Favored : 87.91 % 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: 1.70 (0.31), residues: 725 helix: 2.58 (0.29), residues: 310 sheet: -0.28 (0.47), residues: 105 loop : 0.20 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.004 0.001 HIS A 559 PHE 0.013 0.001 PHE B 452 TYR 0.019 0.001 TYR A 494 ARG 0.002 0.000 ARG A 309 *********************** 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 93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.720 Fit side-chains REVERT: A 377 ASP cc_start: 0.8364 (m-30) cc_final: 0.8163 (m-30) REVERT: A 383 ASN cc_start: 0.8307 (m110) cc_final: 0.7870 (p0) REVERT: A 390 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: A 504 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 376 GLU cc_start: 0.7281 (mp0) cc_final: 0.7070 (mp0) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.1677 time to fit residues: 19.9467 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 433 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6182 Z= 0.255 Angle : 0.517 7.030 8370 Z= 0.262 Chirality : 0.040 0.172 947 Planarity : 0.004 0.040 1056 Dihedral : 4.919 80.824 818 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.54 % Allowed : 9.85 % 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: 1.66 (0.31), residues: 725 helix: 2.57 (0.28), residues: 310 sheet: -0.29 (0.48), residues: 105 loop : 0.15 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.012 0.001 PHE B 452 TYR 0.019 0.001 TYR A 494 ARG 0.005 0.000 ARG B 541 *********************** 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 93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.657 Fit side-chains REVERT: A 383 ASN cc_start: 0.8314 (m110) cc_final: 0.7832 (p0) REVERT: A 390 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: A 504 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 376 GLU cc_start: 0.7272 (mp0) cc_final: 0.7060 (mp0) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.1715 time to fit residues: 20.3100 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 : 0.798 ------------------------------------------------------------------------------- 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 433 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.3980 chunk 66 optimal weight: 0.2980 chunk 68 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6182 Z= 0.204 Angle : 0.506 7.007 8370 Z= 0.257 Chirality : 0.040 0.169 947 Planarity : 0.004 0.041 1056 Dihedral : 4.852 80.141 818 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.24 % Allowed : 10.00 % Favored : 87.76 % 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: 2.68 (0.28), residues: 310 sheet: -0.23 (0.48), residues: 105 loop : 0.16 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.010 0.001 PHE B 452 TYR 0.021 0.001 TYR A 494 ARG 0.004 0.000 ARG B 541 *********************** 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 94 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.685 Fit side-chains REVERT: A 383 ASN cc_start: 0.8274 (m110) cc_final: 0.7742 (p0) REVERT: A 390 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: A 504 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 376 GLU cc_start: 0.7269 (mp0) cc_final: 0.7064 (mp0) outliers start: 15 outliers final: 14 residues processed: 86 average time/residue: 0.1672 time to fit residues: 19.8755 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 : 0.712 ------------------------------------------------------------------------------- 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 290 MET 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 433 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU 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 33 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 339 ASN B 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2841 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= 0.203 Angle : 0.508 6.910 8370 Z= 0.257 Chirality : 0.040 0.168 947 Planarity : 0.004 0.042 1056 Dihedral : 4.817 79.123 818 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.39 % Allowed : 10.00 % 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: 1.80 (0.31), residues: 725 helix: 2.72 (0.29), residues: 310 sheet: -0.19 (0.49), residues: 105 loop : 0.18 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.002 0.001 HIS A 559 PHE 0.010 0.001 PHE B 452 TYR 0.021 0.001 TYR A 494 ARG 0.004 0.000 ARG B 541 ********************** 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 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.724 Fit side-chains REVERT: A 383 ASN cc_start: 0.8248 (m110) cc_final: 0.7737 (p0) REVERT: A 390 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: A 504 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 376 GLU cc_start: 0.7266 (mp0) cc_final: 0.7063 (mp0) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.1534 time to fit residues: 18.5151 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 : 0.620 ------------------------------------------------------------------------------- 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 433 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.0030 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113442 restraints weight = 8317.324| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.59 r_work: 0.3210 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2899 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= 0.208 Angle : 0.516 7.163 8370 Z= 0.261 Chirality : 0.040 0.168 947 Planarity : 0.004 0.042 1056 Dihedral : 4.807 78.486 818 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 10.60 % 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 (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: 1.81 (0.31), residues: 725 helix: 2.72 (0.29), residues: 310 sheet: -0.15 (0.49), residues: 105 loop : 0.17 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.011 0.001 PHE B 452 TYR 0.021 0.001 TYR A 494 ARG 0.004 0.000 ARG B 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.55 seconds wall clock time: 33 minutes 4.02 seconds (1984.02 seconds total)