Starting phenix.real_space_refine on Thu Oct 22 21:29:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.map" model { file = "/net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wuu_66271/10_2026/9wuu_66271.cif" } resolution = 3.35 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 146 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 36 5.16 5 C 3613 2.51 5 N 955 2.21 5 O 1017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5623 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 2852 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 23, 'TRANS': 334} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 358, 2852 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 23, 'TRANS': 334} Chain breaks: 4 bond proxies already assigned to first conformer: 2911 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2761 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 23, 'TRANS': 321} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.72, per 1000 atoms: 0.31 Number of scatterers: 5623 At special positions: 0 Unit cell: (70.14, 85.504, 102.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 36 16.00 P 1 15.00 O 1017 8.00 N 955 7.00 C 3613 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 387.5 milliseconds 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 45.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 207 through 217 removed outlier: 3.803A pdb=" N LEU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.717A pdb=" N GLU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 310 through 330 removed outlier: 3.605A pdb=" N LEU B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.982A pdb=" N MET B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 422 removed outlier: 3.798A pdb=" N TYR B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.504A pdb=" N ALA B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.537A pdb=" N ASN B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.623A pdb=" N LYS B 492 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 517 removed outlier: 3.506A pdb=" N ILE B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 549 removed outlier: 3.736A pdb=" N ILE B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.705A pdb=" N GLN B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.708A pdb=" N ALA A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 4.080A pdb=" N GLU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.745A pdb=" N TRP A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.805A pdb=" N SER A 432 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 433 " --> pdb=" O GLY A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 433' Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.853A pdb=" N LEU A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.622A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.871A pdb=" N ARG A 470 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 4.280A pdb=" N CYS A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.983A pdb=" N LYS A 492 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.506A pdb=" N ILE A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 520 removed outlier: 3.784A pdb=" N ILE A 520 " --> pdb=" O GLU A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 536 through 549 removed outlier: 3.800A pdb=" N ARG A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 4.034A pdb=" N TRP A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AA2, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.692A pdb=" N CYS B 299 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.254A pdb=" N SER B 402 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 199 removed outlier: 3.607A pdb=" N MET A 197 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS A 295 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 253 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 258 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 removed outlier: 5.114A pdb=" N SER A 348 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.513A pdb=" N SER A 402 " --> pdb=" O TYR A 375 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 573 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: 0.74 Time building geometry restraints manager: 0.65 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: 1791 1.34 - 1.46: 1017 1.46 - 1.57: 2891 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 5759 Sorted by residual: bond pdb=" C LEU B 373 " pdb=" O LEU B 373 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.09e-01 bond pdb=" CB LYS B 496 " pdb=" CG LYS B 496 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.10e-01 bond pdb=" CB LYS A 440 " pdb=" CG LYS A 440 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.90e-01 bond pdb=" CB GLU A 379 " pdb=" CG GLU A 379 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.50e-01 bond pdb=" CB PRO A 220 " pdb=" CG PRO A 220 " ideal model delta sigma weight residual 1.492 1.459 0.033 5.00e-02 4.00e+02 4.48e-01 ... (remaining 5754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 7590 1.20 - 2.39: 172 2.39 - 3.59: 56 3.59 - 4.79: 11 4.79 - 5.98: 3 Bond angle restraints: 7832 Sorted by residual: angle pdb=" CA TYR A 191 " pdb=" C TYR A 191 " pdb=" N PRO A 192 " ideal model delta sigma weight residual 118.44 121.81 -3.37 1.59e+00 3.96e-01 4.49e+00 angle pdb=" CB LYS B 496 " pdb=" CG LYS B 496 " pdb=" CD LYS B 496 " ideal model delta sigma weight residual 111.30 115.97 -4.67 2.30e+00 1.89e-01 4.13e+00 angle pdb=" CA TYR A 191 " pdb=" CB TYR A 191 " pdb=" CG TYR A 191 " ideal model delta sigma weight residual 113.90 117.50 -3.60 1.80e+00 3.09e-01 3.99e+00 angle pdb=" CB LYS A 440 " pdb=" CG LYS A 440 " pdb=" CD LYS A 440 " ideal model delta sigma weight residual 111.30 115.90 -4.60 2.30e+00 1.89e-01 3.99e+00 angle pdb=" C ASN B 438 " pdb=" N TYR B 439 " pdb=" CA TYR B 439 " ideal model delta sigma weight residual 121.66 118.29 3.37 1.92e+00 2.71e-01 3.09e+00 ... (remaining 7827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3132 17.97 - 35.93: 293 35.93 - 53.89: 55 53.89 - 71.86: 2 71.86 - 89.82: 5 Dihedral angle restraints: 3487 sinusoidal: 1409 harmonic: 2078 Sorted by residual: dihedral pdb=" CB GLU B 217 " pdb=" CG GLU B 217 " pdb=" CD GLU B 217 " pdb=" OE1 GLU B 217 " ideal model delta sinusoidal sigma weight residual 0.00 89.82 -89.82 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 222 " pdb=" CD ARG A 222 " pdb=" NE ARG A 222 " pdb=" CZ ARG A 222 " ideal model delta sinusoidal sigma weight residual -180.00 -137.11 -42.89 2 1.50e+01 4.44e-03 9.88e+00 dihedral pdb=" CA GLN A 481 " pdb=" C GLN A 481 " pdb=" N LEU A 482 " pdb=" CA LEU A 482 " ideal model delta harmonic sigma weight residual 180.00 164.61 15.39 0 5.00e+00 4.00e-02 9.47e+00 ... (remaining 3484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 635 0.039 - 0.078: 197 0.078 - 0.118: 42 0.118 - 0.157: 8 0.157 - 0.196: 1 Chirality restraints: 883 Sorted by residual: chirality pdb=" CB THR A 400 " pdb=" CA THR A 400 " pdb=" OG1 THR A 400 " pdb=" CG2 THR A 400 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA TYR A 191 " pdb=" N TYR A 191 " pdb=" C TYR A 191 " pdb=" CB TYR A 191 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A 253 " pdb=" N ILE A 253 " pdb=" C ILE A 253 " pdb=" CB ILE A 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 880 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 466 " -0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO A 467 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 247 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 248 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 248 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 248 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 247 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 248 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.021 5.00e-02 4.00e+02 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 955 2.77 - 3.30: 5168 3.30 - 3.83: 8391 3.83 - 4.37: 10240 4.37 - 4.90: 17629 Nonbonded interactions: 42383 Sorted by model distance: nonbonded pdb=" OD2 ASP A 346 " pdb=" OG SER A 348 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 439 " pdb=" O LEU A 463 " model vdw 2.252 3.040 nonbonded pdb=" O LYS B 408 " pdb=" NH1 ARG B 470 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG A 312 " pdb=" OE2 GLU A 539 " model vdw 2.300 3.120 nonbonded pdb=" O SER A 205 " pdb=" OG SER A 205 " model vdw 2.301 3.040 ... (remaining 42378 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 189 or resid 191 through 204 or resid 206 through 239 or r \ esid 241 through 518 or resid 530 through 567)) selection = (chain 'B' and (resid 173 or resid 191 through 204 or resid 206 through 239 or r \ esid 241 through 567)) } 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=0.50 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 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: 7.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.003 0.033 5760 Z= 0.105 Angle : 0.509 5.984 7832 Z= 0.257 Chirality : 0.040 0.196 883 Planarity : 0.005 0.098 992 Dihedral : 13.859 89.823 2135 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.39 % Favored : 95.47 % Rotamer: Outliers : 0.32 % Allowed : 0.16 % Favored : 99.52 % 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: -1.47 (0.33), residues: 685 helix: -1.03 (0.32), residues: 254 sheet: -1.07 (0.54), residues: 95 loop : -0.75 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.011 0.001 TYR B 378 PHE 0.007 0.001 PHE A 437 TRP 0.010 0.001 TRP B 561 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.10 ( 5759) covalent geometry : angle 0.50933 / 0.26 ( 7832) hydrogen bonds : bond 0.30986 / 18.69 ( 202) hydrogen bonds : angle 8.05205 / 5.61 ( 573) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.168 Fit side-chains REVERT: B 508 LEU cc_start: 0.8535 (mp) cc_final: 0.8321 (mp) REVERT: A 355 LEU cc_start: 0.7905 (tt) cc_final: 0.7682 (tt) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0698 time to fit residues: 7.4215 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.2985 > 50:) overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138635 restraints weight = 9322.803| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.73 r_work: 0.3359 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5760 Z= 0.131 Angle : 0.578 6.178 7832 Z= 0.289 Chirality : 0.042 0.131 883 Planarity : 0.005 0.057 992 Dihedral : 5.023 74.795 762 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 0.96 % Allowed : 6.89 % Favored : 92.15 % 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: -0.51 (0.33), residues: 685 helix: 0.40 (0.33), residues: 268 sheet: -0.83 (0.52), residues: 93 loop : -0.72 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.015 0.001 TYR B 540 PHE 0.017 0.001 PHE A 437 TRP 0.008 0.001 TRP A 412 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5759) covalent geometry : angle 0.57771 / 0.29 ( 7832) hydrogen bonds : bond 0.04894 / 3.16 ( 202) hydrogen bonds : angle 4.52462 / 3.18 ( 573) Misc. bond : bond 0.00140 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.222 Fit side-chains REVERT: B 201 TYR cc_start: 0.5612 (p90) cc_final: 0.4218 (t80) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.0756 time to fit residues: 7.3988 Evaluate side-chains 66 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain A residue 341 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [55, 43, 0, 13, 42, 25, 2, 39, 59, 14, 66] chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.171483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133610 restraints weight = 7385.292| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.36 r_work: 0.3351 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5760 Z= 0.168 Angle : 0.579 6.162 7832 Z= 0.284 Chirality : 0.042 0.133 883 Planarity : 0.005 0.046 992 Dihedral : 5.113 74.168 762 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 0.48 % Allowed : 10.42 % Favored : 89.10 % 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: -0.27 (0.34), residues: 685 helix: 0.80 (0.34), residues: 270 sheet: -0.57 (0.56), residues: 87 loop : -0.85 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 241 TYR 0.011 0.001 TYR B 297 PHE 0.013 0.001 PHE B 291 TRP 0.011 0.001 TRP B 412 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 5759) covalent geometry : angle 0.57940 / 0.28 ( 7832) hydrogen bonds : bond 0.05007 / 3.27 ( 202) hydrogen bonds : angle 4.16062 / 2.90 ( 573) Misc. bond : bond 0.00099 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.156 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.0626 time to fit residues: 6.0767 Evaluate side-chains 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain A residue 341 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [38, 1, 23, 46, 41, 65, 43, 52, 56, 44, 10] chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137933 restraints weight = 9525.295| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.98 r_work: 0.3324 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5760 Z= 0.135 Angle : 0.547 7.554 7832 Z= 0.268 Chirality : 0.041 0.132 883 Planarity : 0.005 0.046 992 Dihedral : 5.030 73.160 762 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 1.12 % Allowed : 12.50 % Favored : 86.38 % 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: -0.11 (0.34), residues: 685 helix: 0.99 (0.34), residues: 271 sheet: -0.44 (0.58), residues: 87 loop : -0.85 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.011 0.001 TYR B 378 PHE 0.017 0.001 PHE B 193 TRP 0.030 0.001 TRP A 233 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5759) covalent geometry : angle 0.54662 / 0.27 ( 7832) hydrogen bonds : bond 0.04022 / 2.64 ( 202) hydrogen bonds : angle 3.93060 / 2.75 ( 573) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.224 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.0686 time to fit residues: 6.5158 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 372 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [5, 4, 22, 53, 21, 65, 52, 51, 8, 35, 29] chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135874 restraints weight = 10025.043| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.25 r_work: 0.3317 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5760 Z= 0.092 Angle : 0.505 7.235 7832 Z= 0.246 Chirality : 0.039 0.128 883 Planarity : 0.004 0.045 992 Dihedral : 4.846 74.045 762 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 1.28 % Allowed : 12.82 % Favored : 85.90 % 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: 0.17 (0.34), residues: 685 helix: 1.30 (0.34), residues: 271 sheet: -0.43 (0.56), residues: 93 loop : -0.72 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.010 0.001 TYR B 177 PHE 0.012 0.001 PHE B 193 TRP 0.011 0.001 TRP A 233 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 ( 5759) covalent geometry : angle 0.50476 / 0.25 ( 7832) hydrogen bonds : bond 0.03067 / 2.02 ( 202) hydrogen bonds : angle 3.62854 / 2.53 ( 573) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.224 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.0620 time to fit residues: 6.3655 Evaluate side-chains 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [3, 66, 62, 15, 57, 2, 61, 47, 8, 17, 33] chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139307 restraints weight = 11241.844| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.82 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5760 Z= 0.124 Angle : 0.528 7.812 7832 Z= 0.256 Chirality : 0.041 0.238 883 Planarity : 0.004 0.044 992 Dihedral : 4.869 73.660 762 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 1.44 % Allowed : 12.66 % Favored : 85.90 % 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: 0.11 (0.34), residues: 685 helix: 1.25 (0.34), residues: 271 sheet: -0.45 (0.56), residues: 93 loop : -0.75 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.011 0.001 TYR B 378 PHE 0.018 0.001 PHE A 257 TRP 0.010 0.001 TRP B 412 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.12 ( 5759) covalent geometry : angle 0.52813 / 0.26 ( 7832) hydrogen bonds : bond 0.03552 / 2.35 ( 202) hydrogen bonds : angle 3.60426 / 2.52 ( 573) Misc. bond : bond 0.00075 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.190 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.0673 time to fit residues: 6.6187 Evaluate side-chains 69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [2, 62, 1, 64, 58, 68, 22, 8, 53, 32, 48] chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.174176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130473 restraints weight = 16033.662| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.77 r_work: 0.3311 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5760 Z= 0.106 Angle : 0.510 7.958 7832 Z= 0.248 Chirality : 0.040 0.216 883 Planarity : 0.004 0.044 992 Dihedral : 4.813 73.819 762 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 1.28 % Allowed : 13.78 % Favored : 84.94 % 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: 0.18 (0.34), residues: 685 helix: 1.34 (0.34), residues: 271 sheet: -0.44 (0.55), residues: 93 loop : -0.72 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 336 TYR 0.009 0.001 TYR B 177 PHE 0.014 0.001 PHE A 257 TRP 0.008 0.001 TRP B 412 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 5759) covalent geometry : angle 0.50974 / 0.25 ( 7832) hydrogen bonds : bond 0.03247 / 2.13 ( 202) hydrogen bonds : angle 3.48602 / 2.43 ( 573) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.159 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.0675 time to fit residues: 6.7942 Evaluate side-chains 71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [14, 28, 42, 50, 11, 7, 46, 31, 13, 56, 45] chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131475 restraints weight = 19228.207| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.20 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5760 Z= 0.114 Angle : 0.524 8.062 7832 Z= 0.254 Chirality : 0.040 0.202 883 Planarity : 0.004 0.044 992 Dihedral : 4.810 73.737 762 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.82 % Favored : 95.03 % Rotamer: Outliers : 1.28 % Allowed : 13.78 % Favored : 84.94 % 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: 0.23 (0.34), residues: 685 helix: 1.41 (0.34), residues: 271 sheet: -0.46 (0.55), residues: 93 loop : -0.72 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.012 0.001 TYR B 378 PHE 0.014 0.001 PHE A 257 TRP 0.009 0.001 TRP B 412 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.11 ( 5759) covalent geometry : angle 0.52420 / 0.25 ( 7832) hydrogen bonds : bond 0.03319 / 2.19 ( 202) hydrogen bonds : angle 3.46893 / 2.43 ( 573) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.213 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.0622 time to fit residues: 6.2616 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [28, 52, 49, 0, 3, 15, 63, 21, 45, 14, 67] chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 63 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 HIS A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132729 restraints weight = 16010.475| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.96 r_work: 0.3296 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5760 Z= 0.112 Angle : 0.520 8.068 7832 Z= 0.252 Chirality : 0.040 0.200 883 Planarity : 0.004 0.044 992 Dihedral : 4.801 73.847 762 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 1.44 % Allowed : 13.94 % Favored : 84.62 % 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: 0.31 (0.34), residues: 685 helix: 1.56 (0.34), residues: 268 sheet: -0.54 (0.54), residues: 95 loop : -0.70 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.009 0.001 TYR B 177 PHE 0.010 0.001 PHE A 257 TRP 0.009 0.001 TRP B 412 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 5759) covalent geometry : angle 0.51970 / 0.25 ( 7832) hydrogen bonds : bond 0.03263 / 2.16 ( 202) hydrogen bonds : angle 3.42209 / 2.41 ( 573) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.224 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0661 time to fit residues: 6.7349 Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [30, 57, 40, 20, 58, 67, 24, 35, 62, 44, 28] chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 35 optimal weight: 8.9990 chunk 62 optimal weight: 0.0000 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152167 restraints weight = 10180.045| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.76 r_work: 0.3575 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5760 Z= 0.087 Angle : 0.500 8.110 7832 Z= 0.243 Chirality : 0.039 0.194 883 Planarity : 0.004 0.043 992 Dihedral : 4.665 74.361 762 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 0.96 % Allowed : 14.26 % Favored : 84.78 % 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: 0.49 (0.35), residues: 685 helix: 1.67 (0.34), residues: 271 sheet: -0.37 (0.54), residues: 96 loop : -0.59 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.013 0.001 TYR B 378 PHE 0.009 0.001 PHE A 257 TRP 0.053 0.002 TRP A 233 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 5759) covalent geometry : angle 0.50003 / 0.24 ( 7832) hydrogen bonds : bond 0.02535 / 1.67 ( 202) hydrogen bonds : angle 3.34827 / 2.35 ( 573) Misc. bond : bond 0.00059 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.225 Fit side-chains REVERT: B 504 LEU cc_start: 0.8881 (mt) cc_final: 0.8583 (tp) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.0731 time to fit residues: 7.0444 Evaluate side-chains 70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 536 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: [59, 14, 41, 24, 67, 42, 15, 7, 49, 39, 60] chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133579 restraints weight = 15989.805| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.97 r_work: 0.3309 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5760 Z= 0.099 Angle : 0.507 8.026 7832 Z= 0.245 Chirality : 0.040 0.189 883 Planarity : 0.004 0.043 992 Dihedral : 4.705 74.696 762 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 0.96 % Allowed : 14.58 % Favored : 84.46 % 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: 0.49 (0.35), residues: 685 helix: 1.67 (0.34), residues: 271 sheet: -0.39 (0.55), residues: 95 loop : -0.60 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.009 0.001 TYR B 177 PHE 0.010 0.001 PHE A 257 TRP 0.044 0.001 TRP A 233 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 5759) covalent geometry : angle 0.50699 / 0.24 ( 7832) hydrogen bonds : bond 0.02909 / 1.93 ( 202) hydrogen bonds : angle 3.33627 / 2.35 ( 573) Misc. bond : bond 0.00044 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.05 seconds wall clock time: 25 minutes 50.80 seconds (1550.80 seconds total)