Starting phenix.real_space_refine on Sun Apr 27 06:50:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykj_33892/04_2025/7ykj_33892.cif" } resolution = 3.5 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= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3072 2.51 5 N 810 2.21 5 O 906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4811 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1529 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1556 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 906 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.06, per 1000 atoms: 0.84 Number of scatterers: 4811 At special positions: 0 Unit cell: (73.14, 112.36, 95.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 906 8.00 N 810 7.00 C 3072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.06 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.02 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: 1.19 Conformation dependent library (CDL) restraints added in 575.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1154 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 13.6% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.828A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.034A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.702A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.538A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.802A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.708A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.379A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.206A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 29 through 33 removed outlier: 4.178A pdb=" N SER D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.769A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.082A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.017A pdb=" N CYS A 96 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 111 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS A 98 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.676A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 333 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: 1.26 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1077 1.33 - 1.45: 1243 1.45 - 1.58: 2596 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 4941 Sorted by residual: bond pdb=" N ILE D 59 " pdb=" CA ILE D 59 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.74e+01 bond pdb=" CE1 HIS B 505 " pdb=" NE2 HIS B 505 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.70e+01 bond pdb=" CE1 HIS C 505 " pdb=" NE2 HIS C 505 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N SER B 446 " pdb=" CA SER B 446 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.16e-02 7.43e+03 9.81e+00 ... (remaining 4936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 5832 2.67 - 5.35: 858 5.35 - 8.02: 42 8.02 - 10.70: 4 10.70 - 13.37: 2 Bond angle restraints: 6738 Sorted by residual: angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 98.63 13.37 1.40e+00 5.10e-01 9.12e+01 angle pdb=" OD1 ASN A 74 " pdb=" CG ASN A 74 " pdb=" ND2 ASN A 74 " ideal model delta sigma weight residual 122.60 117.20 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" OE1 GLN C 409 " pdb=" CD GLN C 409 " pdb=" NE2 GLN C 409 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" OD1 ASN C 439 " pdb=" CG ASN C 439 " pdb=" ND2 ASN C 439 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.70e+01 angle pdb=" OD1 ASN C 394 " pdb=" CG ASN C 394 " pdb=" ND2 ASN C 394 " ideal model delta sigma weight residual 122.60 117.49 5.11 1.00e+00 1.00e+00 2.61e+01 ... (remaining 6733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2552 17.52 - 35.04: 277 35.04 - 52.56: 54 52.56 - 70.08: 12 70.08 - 87.60: 6 Dihedral angle restraints: 2901 sinusoidal: 1082 harmonic: 1819 Sorted by residual: dihedral pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " pdb=" NH1 ARG B 466 " ideal model delta sinusoidal sigma weight residual 0.00 87.60 -87.60 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CA SER D 95 " pdb=" C SER D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual -180.00 -134.01 -45.99 0 5.00e+00 4.00e-02 8.46e+01 dihedral pdb=" CD ARG C 498 " pdb=" NE ARG C 498 " pdb=" CZ ARG C 498 " pdb=" NH1 ARG C 498 " ideal model delta sinusoidal sigma weight residual 0.00 -82.34 82.34 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 2898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 525 0.095 - 0.190: 167 0.190 - 0.285: 31 0.285 - 0.380: 4 0.380 - 0.475: 1 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA THR D 5 " pdb=" N THR D 5 " pdb=" C THR D 5 " pdb=" CB THR D 5 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB THR A 115 " pdb=" CA THR A 115 " pdb=" OG1 THR A 115 " pdb=" CG2 THR A 115 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 725 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 32 " 0.175 2.00e-02 2.50e+03 9.32e-02 1.74e+02 pdb=" CG TYR A 32 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR A 32 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR A 32 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR A 32 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 32 " -0.038 2.00e-02 2.50e+03 pdb=" CZ TYR A 32 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 32 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 109 " 0.061 2.00e-02 2.50e+03 1.26e-01 1.59e+02 pdb=" CG ASP A 109 " -0.218 2.00e-02 2.50e+03 pdb=" OD1 ASP A 109 " 0.079 2.00e-02 2.50e+03 pdb=" OD2 ASP A 109 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " 0.128 2.00e-02 2.50e+03 7.75e-02 1.50e+02 pdb=" CG TRP A 36 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " -0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " 0.107 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " -0.089 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " 0.073 2.00e-02 2.50e+03 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 5 2.39 - 3.02: 2646 3.02 - 3.64: 6997 3.64 - 4.27: 10751 4.27 - 4.90: 17483 Nonbonded interactions: 37882 Sorted by model distance: nonbonded pdb=" O TYR C 495 " pdb=" OG SER C 496 " model vdw 1.761 3.040 nonbonded pdb=" OG SER A 101 " pdb=" O TYR A 103 " model vdw 2.026 3.040 nonbonded pdb=" OG1 THR A 54 " pdb=" OD1 ASP A 56 " model vdw 2.284 3.040 nonbonded pdb=" O PRO D 96 " pdb=" N LEU D 98 " model vdw 2.286 3.120 nonbonded pdb=" NH1 ARG D 55 " pdb=" O PHE D 63 " model vdw 2.356 3.120 ... (remaining 37877 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 'B' and (resid 331 through 374 or (resid 375 through 377 and (name N or n \ ame CA or name C or name O or name CB )) or resid 378 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 49 \ 2 or (resid 493 and (name N or name CA or name C or name O or name CB )) or resi \ d 494 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 528)) selection = (chain 'C' and (resid 331 through 345 or (resid 346 through 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 357 or (resid 358 \ and (name N or name CA or name C or name O or name CB )) or resid 359 through 37 \ 5 or (resid 376 through 377 and (name N or name CA or name C or name O or name C \ B )) or resid 378 through 423 or (resid 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 445 or (resid 446 and \ (name N or name CA or name C or name O or name CB )) or resid 447 through 451 or \ (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 3 through 480 or (resid 481 and (name N or name CA or name C or name O or name C \ B )) or resid 482 through 495 or (resid 496 and (name N or name CA or name C or \ name O or name CB )) or resid 497 or (resid 498 and (name N or name CA or name C \ or name O or name CB )) or resid 499 through 528)) } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.770 Find NCS groups from input model: 0.130 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 : 0.013 0.058 4950 Z= 0.783 Angle : 1.781 13.371 6756 Z= 1.181 Chirality : 0.095 0.475 728 Planarity : 0.040 0.488 878 Dihedral : 15.542 87.598 1720 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 1.13 % Allowed : 6.63 % Favored : 92.23 % Rotamer: Outliers : 2.98 % Allowed : 16.70 % Favored : 80.32 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 618 helix: -4.60 (0.38), residues: 42 sheet: -1.24 (0.41), residues: 148 loop : -1.57 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.128 0.026 TRP A 36 HIS 0.019 0.004 HIS A 59 PHE 0.045 0.008 PHE A 27 TYR 0.175 0.020 TYR A 32 ARG 0.040 0.003 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.22438 ( 140) hydrogen bonds : angle 10.09743 ( 333) SS BOND : bond 0.01631 ( 9) SS BOND : angle 1.87069 ( 18) covalent geometry : bond 0.01301 ( 4941) covalent geometry : angle 1.78074 ( 6738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.520 Fit side-chains REVERT: B 400 PHE cc_start: 0.6246 (p90) cc_final: 0.5878 (p90) REVERT: A 28 THR cc_start: 0.9157 (m) cc_final: 0.8909 (p) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 0.2209 time to fit residues: 34.3597 Evaluate side-chains 89 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.175184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128521 restraints weight = 9639.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131498 restraints weight = 5548.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133489 restraints weight = 3948.564| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4950 Z= 0.150 Angle : 0.676 6.743 6756 Z= 0.355 Chirality : 0.047 0.200 728 Planarity : 0.006 0.063 878 Dihedral : 6.107 43.639 702 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.02 % Favored : 94.34 % Rotamer: Outliers : 4.77 % Allowed : 18.29 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.34), residues: 618 helix: -3.86 (0.49), residues: 43 sheet: -1.15 (0.38), residues: 150 loop : -0.76 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.003 0.001 HIS C 519 PHE 0.012 0.001 PHE D 100 TYR 0.016 0.002 TYR A 103 ARG 0.004 0.001 ARG C 408 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 140) hydrogen bonds : angle 7.30785 ( 333) SS BOND : bond 0.00510 ( 9) SS BOND : angle 1.05345 ( 18) covalent geometry : bond 0.00345 ( 4941) covalent geometry : angle 0.67509 ( 6738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.500 Fit side-chains REVERT: B 400 PHE cc_start: 0.6167 (p90) cc_final: 0.5907 (p90) REVERT: B 418 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6867 (mm) REVERT: B 457 ARG cc_start: 0.4909 (ttt-90) cc_final: 0.4657 (ttt180) REVERT: A 3 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6819 (pp30) REVERT: A 28 THR cc_start: 0.9071 (m) cc_final: 0.8665 (p) REVERT: A 57 ASP cc_start: 0.7958 (t70) cc_final: 0.7654 (t70) REVERT: A 95 TYR cc_start: 0.8572 (m-80) cc_final: 0.8184 (m-80) outliers start: 24 outliers final: 12 residues processed: 125 average time/residue: 0.1947 time to fit residues: 29.8616 Evaluate side-chains 101 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN D 38 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124270 restraints weight = 9450.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126665 restraints weight = 5991.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128182 restraints weight = 4496.371| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 4950 Z= 0.237 Angle : 0.752 9.605 6756 Z= 0.391 Chirality : 0.049 0.201 728 Planarity : 0.006 0.066 878 Dihedral : 6.151 44.661 696 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.63 % Favored : 92.56 % Rotamer: Outliers : 7.36 % Allowed : 18.69 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 618 helix: -3.42 (0.57), residues: 43 sheet: -0.72 (0.39), residues: 160 loop : -1.06 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 111 HIS 0.002 0.001 HIS B 519 PHE 0.016 0.002 PHE B 338 TYR 0.023 0.002 TYR A 60 ARG 0.004 0.001 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 140) hydrogen bonds : angle 6.90036 ( 333) SS BOND : bond 0.00790 ( 9) SS BOND : angle 2.78468 ( 18) covalent geometry : bond 0.00561 ( 4941) covalent geometry : angle 0.73889 ( 6738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.562 Fit side-chains REVERT: B 369 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4950 (p90) REVERT: B 418 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6856 (mm) REVERT: A 32 TYR cc_start: 0.7862 (m-80) cc_final: 0.7350 (m-10) REVERT: A 57 ASP cc_start: 0.8023 (t70) cc_final: 0.7767 (t70) REVERT: A 84 ASN cc_start: 0.7985 (p0) cc_final: 0.7640 (m-40) REVERT: A 95 TYR cc_start: 0.8550 (m-80) cc_final: 0.8336 (m-80) outliers start: 37 outliers final: 24 residues processed: 116 average time/residue: 0.1784 time to fit residues: 26.3165 Evaluate side-chains 110 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 0.0370 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 HIS ** C 422 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.171500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126750 restraints weight = 9662.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129254 restraints weight = 5987.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130976 restraints weight = 4455.937| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4950 Z= 0.161 Angle : 0.658 8.497 6756 Z= 0.339 Chirality : 0.047 0.213 728 Planarity : 0.005 0.066 878 Dihedral : 5.732 43.174 696 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.18 % Favored : 94.17 % Rotamer: Outliers : 6.76 % Allowed : 20.28 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.57 (0.34), residues: 618 helix: -2.85 (0.69), residues: 43 sheet: -0.54 (0.41), residues: 156 loop : -1.06 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 111 HIS 0.002 0.001 HIS B 519 PHE 0.010 0.001 PHE D 100 TYR 0.016 0.002 TYR D 37 ARG 0.003 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 140) hydrogen bonds : angle 6.42277 ( 333) SS BOND : bond 0.00409 ( 9) SS BOND : angle 2.09496 ( 18) covalent geometry : bond 0.00379 ( 4941) covalent geometry : angle 0.65019 ( 6738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.608 Fit side-chains REVERT: B 369 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5001 (p90) REVERT: B 403 ARG cc_start: 0.4944 (OUTLIER) cc_final: 0.4646 (ptm-80) REVERT: B 418 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6968 (mm) REVERT: B 457 ARG cc_start: 0.5116 (ttt-90) cc_final: 0.4846 (ttt180) REVERT: A 18 LEU cc_start: 0.7942 (tp) cc_final: 0.7739 (mt) REVERT: A 32 TYR cc_start: 0.7777 (m-80) cc_final: 0.7356 (m-10) REVERT: A 57 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7653 (t70) REVERT: D 55 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8038 (ttm110) outliers start: 34 outliers final: 24 residues processed: 117 average time/residue: 0.2541 time to fit residues: 36.9128 Evaluate side-chains 116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.172623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128571 restraints weight = 9661.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131148 restraints weight = 5942.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132876 restraints weight = 4319.002| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4950 Z= 0.122 Angle : 0.623 7.321 6756 Z= 0.321 Chirality : 0.046 0.277 728 Planarity : 0.005 0.060 878 Dihedral : 5.443 38.790 696 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.66 % Favored : 93.85 % Rotamer: Outliers : 5.37 % Allowed : 22.07 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.37 (0.34), residues: 618 helix: -2.96 (0.74), residues: 37 sheet: -0.42 (0.41), residues: 158 loop : -0.92 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.002 0.001 HIS B 505 PHE 0.009 0.001 PHE D 100 TYR 0.015 0.001 TYR D 37 ARG 0.005 0.001 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 140) hydrogen bonds : angle 6.20441 ( 333) SS BOND : bond 0.00301 ( 9) SS BOND : angle 1.63779 ( 18) covalent geometry : bond 0.00285 ( 4941) covalent geometry : angle 0.61758 ( 6738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.679 Fit side-chains REVERT: B 369 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.4881 (p90) REVERT: B 403 ARG cc_start: 0.4874 (ptm-80) cc_final: 0.4639 (ptm-80) REVERT: A 32 TYR cc_start: 0.7716 (m-80) cc_final: 0.7232 (m-10) REVERT: A 57 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7644 (t70) REVERT: D 87 TYR cc_start: 0.8473 (m-10) cc_final: 0.8239 (m-10) outliers start: 27 outliers final: 17 residues processed: 115 average time/residue: 0.2103 time to fit residues: 30.0321 Evaluate side-chains 109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.174612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130960 restraints weight = 9615.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133434 restraints weight = 5929.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135259 restraints weight = 4322.686| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4950 Z= 0.107 Angle : 0.598 8.204 6756 Z= 0.308 Chirality : 0.046 0.250 728 Planarity : 0.005 0.053 878 Dihedral : 5.164 36.099 696 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.18 % Favored : 94.50 % Rotamer: Outliers : 4.77 % Allowed : 21.87 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.19 (0.35), residues: 618 helix: -2.74 (0.79), residues: 37 sheet: -0.26 (0.41), residues: 156 loop : -0.82 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 105 HIS 0.001 0.000 HIS B 519 PHE 0.008 0.001 PHE D 100 TYR 0.014 0.001 TYR D 37 ARG 0.004 0.000 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 140) hydrogen bonds : angle 5.93754 ( 333) SS BOND : bond 0.00222 ( 9) SS BOND : angle 1.38515 ( 18) covalent geometry : bond 0.00247 ( 4941) covalent geometry : angle 0.59488 ( 6738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.512 Fit side-chains REVERT: B 369 TYR cc_start: 0.5595 (OUTLIER) cc_final: 0.4705 (p90) REVERT: B 403 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.4526 (ptm-80) REVERT: C 467 ASP cc_start: 0.6818 (t0) cc_final: 0.6576 (t0) REVERT: A 18 LEU cc_start: 0.8064 (tp) cc_final: 0.7821 (tp) REVERT: A 32 TYR cc_start: 0.7598 (m-80) cc_final: 0.7152 (m-10) REVERT: A 57 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7523 (t70) REVERT: D 108 ILE cc_start: 0.4648 (OUTLIER) cc_final: 0.4038 (tp) outliers start: 24 outliers final: 17 residues processed: 111 average time/residue: 0.1821 time to fit residues: 25.2364 Evaluate side-chains 113 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.0270 chunk 52 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.171689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127906 restraints weight = 9450.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130345 restraints weight = 5855.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132048 restraints weight = 4304.847| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4950 Z= 0.144 Angle : 0.634 7.792 6756 Z= 0.324 Chirality : 0.046 0.259 728 Planarity : 0.005 0.054 878 Dihedral : 5.258 36.211 696 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.83 % Favored : 93.85 % Rotamer: Outliers : 5.96 % Allowed : 20.87 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.10 (0.35), residues: 618 helix: -2.38 (0.88), residues: 31 sheet: -0.11 (0.42), residues: 156 loop : -0.87 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.001 0.001 HIS B 505 PHE 0.011 0.001 PHE C 377 TYR 0.013 0.001 TYR C 473 ARG 0.005 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 140) hydrogen bonds : angle 5.98244 ( 333) SS BOND : bond 0.00407 ( 9) SS BOND : angle 1.70967 ( 18) covalent geometry : bond 0.00339 ( 4941) covalent geometry : angle 0.62861 ( 6738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.468 Fit side-chains REVERT: B 369 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.4917 (p90) REVERT: B 403 ARG cc_start: 0.4870 (OUTLIER) cc_final: 0.4551 (ptm-80) REVERT: C 467 ASP cc_start: 0.6886 (t0) cc_final: 0.6610 (t0) REVERT: A 18 LEU cc_start: 0.8040 (tp) cc_final: 0.7835 (tp) REVERT: A 32 TYR cc_start: 0.7842 (m-80) cc_final: 0.7327 (m-10) REVERT: A 57 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7687 (t70) REVERT: D 78 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5022 (ptm-80) REVERT: D 108 ILE cc_start: 0.4347 (OUTLIER) cc_final: 0.3732 (tp) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.1955 time to fit residues: 27.0892 Evaluate side-chains 113 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.169190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125090 restraints weight = 9554.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127557 restraints weight = 5947.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129183 restraints weight = 4387.031| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 4950 Z= 0.198 Angle : 0.674 7.788 6756 Z= 0.349 Chirality : 0.047 0.276 728 Planarity : 0.006 0.054 878 Dihedral : 5.547 39.819 696 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.31 % Favored : 93.20 % Rotamer: Outliers : 6.76 % Allowed : 20.48 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.10 (0.35), residues: 618 helix: -2.47 (0.86), residues: 31 sheet: 0.08 (0.42), residues: 163 loop : -0.95 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 111 HIS 0.002 0.001 HIS B 505 PHE 0.016 0.002 PHE C 377 TYR 0.015 0.002 TYR C 473 ARG 0.009 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 140) hydrogen bonds : angle 6.03004 ( 333) SS BOND : bond 0.00540 ( 9) SS BOND : angle 1.87584 ( 18) covalent geometry : bond 0.00473 ( 4941) covalent geometry : angle 0.66838 ( 6738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.565 Fit side-chains REVERT: B 369 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.5128 (p90) REVERT: B 403 ARG cc_start: 0.5001 (OUTLIER) cc_final: 0.4610 (ptm-80) REVERT: C 467 ASP cc_start: 0.6993 (t0) cc_final: 0.6647 (t0) REVERT: A 32 TYR cc_start: 0.7946 (m-80) cc_final: 0.7413 (m-10) REVERT: A 57 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7548 (t70) REVERT: A 103 TYR cc_start: 0.8180 (m-10) cc_final: 0.7898 (m-10) REVERT: D 78 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5138 (ptm-80) REVERT: D 108 ILE cc_start: 0.4182 (OUTLIER) cc_final: 0.3521 (tp) outliers start: 34 outliers final: 26 residues processed: 118 average time/residue: 0.2128 time to fit residues: 31.6579 Evaluate side-chains 122 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.559 > 50: distance: 33 - 37: 19.200 distance: 37 - 38: 13.578 distance: 37 - 147: 21.696 distance: 38 - 39: 8.499 distance: 38 - 41: 19.297 distance: 39 - 40: 19.899 distance: 39 - 49: 26.611 distance: 40 - 144: 23.130 distance: 41 - 42: 12.503 distance: 42 - 43: 6.006 distance: 42 - 44: 18.020 distance: 43 - 45: 8.046 distance: 44 - 46: 13.230 distance: 45 - 47: 11.505 distance: 46 - 47: 10.118 distance: 47 - 48: 22.887 distance: 49 - 50: 6.761 distance: 50 - 51: 5.985 distance: 51 - 52: 14.116 distance: 51 - 53: 8.207 distance: 53 - 54: 8.826 distance: 54 - 55: 19.407 distance: 54 - 57: 21.948 distance: 55 - 56: 18.243 distance: 55 - 60: 16.107 distance: 57 - 58: 16.920 distance: 57 - 59: 34.040 distance: 60 - 61: 21.693 distance: 61 - 62: 3.779 distance: 61 - 64: 16.718 distance: 62 - 63: 34.339 distance: 62 - 66: 32.664 distance: 64 - 65: 42.466 distance: 66 - 67: 22.441 distance: 66 - 72: 30.049 distance: 67 - 68: 25.142 distance: 67 - 70: 12.253 distance: 68 - 69: 17.073 distance: 68 - 73: 36.418 distance: 70 - 71: 41.800 distance: 71 - 72: 13.299 distance: 73 - 74: 16.164 distance: 74 - 75: 20.281 distance: 74 - 77: 18.551 distance: 75 - 76: 20.716 distance: 75 - 80: 31.078 distance: 77 - 78: 23.961 distance: 77 - 79: 20.630 distance: 80 - 81: 10.330 distance: 81 - 82: 23.514 distance: 81 - 84: 18.093 distance: 82 - 83: 16.457 distance: 82 - 89: 20.299 distance: 83 - 105: 14.754 distance: 84 - 85: 22.792 distance: 85 - 86: 10.648 distance: 86 - 87: 16.434 distance: 87 - 88: 27.330 distance: 89 - 90: 5.623 distance: 90 - 91: 8.326 distance: 90 - 93: 3.999 distance: 91 - 92: 16.729 distance: 91 - 97: 6.446 distance: 93 - 94: 10.624 distance: 94 - 95: 8.475 distance: 94 - 96: 9.595 distance: 97 - 98: 8.608 distance: 98 - 99: 4.153 distance: 98 - 101: 8.615 distance: 99 - 100: 8.071 distance: 101 - 102: 6.498 distance: 102 - 103: 7.932 distance: 102 - 104: 12.975 distance: 106 - 107: 12.003 distance: 106 - 109: 5.129 distance: 107 - 113: 11.998 distance: 110 - 111: 7.604 distance: 110 - 112: 10.985