Starting phenix.real_space_refine on Fri Aug 2 19:58:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_33892.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_33892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_33892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_33892.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykj_33892/08_2024/7ykj_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 Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 3.89, per 1000 atoms: 0.81 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 - 3.50 Amino acid : False - 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: 1.48 Conformation dependent library (CDL) restraints added in 806.0 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: 0.67 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: 1.11 Time building geometry restraints manager: 1.68 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: 98.26 - 105.81: 125 105.81 - 113.35: 2288 113.35 - 120.89: 2666 120.89 - 128.43: 1629 128.43 - 135.98: 30 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: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.120 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- 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 4941 Z= 0.844 Angle : 1.781 13.371 6738 Z= 1.182 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.540 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: 0.2159 time to fit residues: 33.4617 Evaluate side-chains 89 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 354 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4941 Z= 0.219 Angle : 0.678 6.455 6738 Z= 0.356 Chirality : 0.047 0.203 728 Planarity : 0.006 0.063 878 Dihedral : 6.103 43.875 702 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.02 % Favored : 94.34 % Rotamer: Outliers : 3.78 % Allowed : 18.89 % Favored : 77.34 % 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: -1.67 (0.34), residues: 618 helix: -3.88 (0.49), residues: 43 sheet: -1.14 (0.38), residues: 152 loop : -0.76 (0.32), residues: 423 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 95 ARG 0.004 0.001 ARG C 408 *********************** 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 128 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.543 Fit side-chains REVERT: B 400 PHE cc_start: 0.6247 (p90) cc_final: 0.6010 (p90) REVERT: B 418 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6786 (mm) REVERT: B 457 ARG cc_start: 0.5068 (ttt-90) cc_final: 0.4825 (ttt180) REVERT: A 28 THR cc_start: 0.9146 (m) cc_final: 0.8766 (p) REVERT: A 32 TYR cc_start: 0.7360 (m-80) cc_final: 0.7098 (m-10) REVERT: A 57 ASP cc_start: 0.7848 (t70) cc_final: 0.7591 (t70) REVERT: A 91 THR cc_start: 0.8347 (m) cc_final: 0.8143 (t) REVERT: A 95 TYR cc_start: 0.8561 (m-80) cc_final: 0.8174 (m-80) outliers start: 19 outliers final: 8 residues processed: 119 average time/residue: 0.2005 time to fit residues: 29.2461 Evaluate side-chains 97 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 23 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 505 HIS C 506 GLN A 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4941 Z= 0.175 Angle : 0.638 11.328 6738 Z= 0.331 Chirality : 0.046 0.202 728 Planarity : 0.005 0.058 878 Dihedral : 5.481 41.650 696 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.66 % Favored : 93.69 % Rotamer: Outliers : 5.77 % Allowed : 18.29 % Favored : 75.94 % 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: -1.44 (0.34), residues: 618 helix: -3.15 (0.61), residues: 43 sheet: -0.86 (0.39), residues: 151 loop : -0.73 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 36 HIS 0.004 0.001 HIS C 505 PHE 0.011 0.001 PHE A 27 TYR 0.022 0.001 TYR A 60 ARG 0.004 0.001 ARG B 357 *********************** 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 129 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.522 Fit side-chains REVERT: B 369 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.4739 (p90) REVERT: B 418 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6924 (mm) REVERT: B 457 ARG cc_start: 0.4997 (ttt-90) cc_final: 0.4698 (ttt-90) REVERT: B 519 HIS cc_start: 0.3736 (OUTLIER) cc_final: 0.3395 (p90) REVERT: A 28 THR cc_start: 0.9102 (m) cc_final: 0.8723 (p) REVERT: A 32 TYR cc_start: 0.7479 (m-80) cc_final: 0.7193 (m-10) REVERT: A 57 ASP cc_start: 0.7807 (t70) cc_final: 0.7566 (t70) REVERT: A 95 TYR cc_start: 0.8493 (m-80) cc_final: 0.8193 (m-80) outliers start: 29 outliers final: 19 residues processed: 119 average time/residue: 0.1763 time to fit residues: 26.4217 Evaluate side-chains 112 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 519 HIS 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 430 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 ASN 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 23 CYS Chi-restraints excluded: chain D residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4941 Z= 0.301 Angle : 0.689 8.381 6738 Z= 0.357 Chirality : 0.047 0.170 728 Planarity : 0.006 0.064 878 Dihedral : 5.765 42.661 696 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.99 % Favored : 93.37 % Rotamer: Outliers : 6.56 % Allowed : 20.08 % 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: -1.53 (0.34), residues: 618 helix: -2.80 (0.67), residues: 44 sheet: -0.55 (0.40), residues: 158 loop : -1.02 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 111 HIS 0.002 0.001 HIS B 505 PHE 0.013 0.002 PHE C 377 TYR 0.018 0.002 TYR C 495 ARG 0.008 0.001 ARG A 19 *********************** 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 128 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.549 Fit side-chains REVERT: B 369 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.5019 (p90) REVERT: A 6 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.7048 (t0) REVERT: A 32 TYR cc_start: 0.7907 (m-80) cc_final: 0.7560 (m-10) REVERT: A 57 ASP cc_start: 0.7947 (t70) cc_final: 0.7644 (t70) outliers start: 33 outliers final: 23 residues processed: 115 average time/residue: 0.1716 time to fit residues: 25.3251 Evaluate side-chains 107 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain B residue 461 LEU 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 393 THR 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 3 GLN Chi-restraints excluded: chain A residue 6 ASP 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 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 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4941 Z= 0.291 Angle : 0.675 8.045 6738 Z= 0.347 Chirality : 0.047 0.181 728 Planarity : 0.005 0.065 878 Dihedral : 5.756 42.621 696 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.47 % Favored : 92.88 % Rotamer: Outliers : 7.55 % Allowed : 20.48 % Favored : 71.97 % 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: -1.58 (0.33), residues: 618 helix: -3.02 (0.74), residues: 37 sheet: -0.52 (0.40), residues: 160 loop : -1.10 (0.31), residues: 421 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 0.015 0.002 TYR D 37 ARG 0.005 0.001 ARG A 19 *********************** 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 fitting. rotamer outliers: 38 poor density : 90 time to evaluate : 0.629 Fit side-chains REVERT: B 369 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.5110 (p90) REVERT: B 461 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5775 (mp) REVERT: A 18 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7222 (mp) REVERT: A 32 TYR cc_start: 0.7818 (m-80) cc_final: 0.7411 (m-10) REVERT: A 57 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7619 (t70) outliers start: 38 outliers final: 26 residues processed: 114 average time/residue: 0.1867 time to fit residues: 26.8734 Evaluate side-chains 112 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 333 THR 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 393 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 C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 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 Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 4941 Z= 0.361 Angle : 0.709 7.840 6738 Z= 0.369 Chirality : 0.048 0.202 728 Planarity : 0.006 0.068 878 Dihedral : 6.015 43.187 696 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.31 % Favored : 93.20 % Rotamer: Outliers : 6.76 % Allowed : 21.07 % Favored : 72.17 % 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: -2.83 (0.73), residues: 37 sheet: -0.62 (0.40), residues: 162 loop : -1.17 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 436 HIS 0.003 0.001 HIS B 505 PHE 0.013 0.002 PHE B 400 TYR 0.017 0.002 TYR C 473 ARG 0.008 0.001 ARG A 19 *********************** 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 129 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 0.551 Fit side-chains REVERT: B 369 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5371 (p90) REVERT: B 461 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5689 (mp) REVERT: C 467 ASP cc_start: 0.6999 (t0) cc_final: 0.6650 (t0) REVERT: A 32 TYR cc_start: 0.7891 (m-80) cc_final: 0.7466 (m-10) REVERT: A 57 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7574 (t70) REVERT: A 103 TYR cc_start: 0.8189 (m-10) cc_final: 0.7919 (m-10) REVERT: D 43 GLN cc_start: 0.8134 (mt0) cc_final: 0.7883 (pm20) REVERT: D 78 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5114 (ptm-80) outliers start: 34 outliers final: 27 residues processed: 115 average time/residue: 0.1799 time to fit residues: 26.0713 Evaluate side-chains 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 HIS 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 393 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 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 12 VAL Chi-restraints excluded: chain A residue 57 ASP 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 23 CYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.0030 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4941 Z= 0.172 Angle : 0.622 6.891 6738 Z= 0.323 Chirality : 0.047 0.209 728 Planarity : 0.005 0.062 878 Dihedral : 5.417 39.345 696 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.18 % Favored : 94.50 % Rotamer: Outliers : 5.37 % Allowed : 23.26 % Favored : 71.37 % 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: -1.56 (0.34), residues: 618 helix: -2.60 (0.73), residues: 43 sheet: -0.43 (0.40), residues: 157 loop : -1.13 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.009 0.001 PHE D 100 TYR 0.014 0.001 TYR A 95 ARG 0.007 0.001 ARG A 19 *********************** 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 125 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.516 Fit side-chains REVERT: B 369 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5270 (p90) REVERT: C 467 ASP cc_start: 0.6791 (t0) cc_final: 0.6487 (t0) REVERT: A 32 TYR cc_start: 0.7758 (m-80) cc_final: 0.7339 (m-10) REVERT: A 57 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7632 (t70) REVERT: D 108 ILE cc_start: 0.4469 (OUTLIER) cc_final: 0.3831 (tp) outliers start: 27 outliers final: 18 residues processed: 113 average time/residue: 0.2032 time to fit residues: 28.2492 Evaluate side-chains 111 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 519 HIS 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 441 LEU Chi-restraints excluded: chain C residue 472 ILE 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 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 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4941 Z= 0.181 Angle : 0.624 6.821 6738 Z= 0.323 Chirality : 0.046 0.171 728 Planarity : 0.005 0.054 878 Dihedral : 5.186 35.631 696 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.66 % Favored : 94.01 % Rotamer: Outliers : 5.37 % Allowed : 22.47 % Favored : 72.17 % 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: -1.39 (0.34), residues: 618 helix: -2.18 (0.81), residues: 37 sheet: -0.42 (0.40), residues: 161 loop : -1.03 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.002 0.000 HIS B 505 PHE 0.007 0.001 PHE C 429 TYR 0.015 0.001 TYR A 95 ARG 0.010 0.001 ARG A 19 *********************** 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 119 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5075 (p90) REVERT: C 362 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7855 (t) REVERT: C 467 ASP cc_start: 0.6851 (t0) cc_final: 0.6533 (t0) REVERT: A 32 TYR cc_start: 0.7743 (m-80) cc_final: 0.7290 (m-10) REVERT: A 57 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7611 (t70) REVERT: D 108 ILE cc_start: 0.4016 (OUTLIER) cc_final: 0.3394 (tp) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 0.1745 time to fit residues: 23.1576 Evaluate side-chains 109 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 362 VAL 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 18 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 23 CYS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 SER 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-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.5199 > 50: distance: 93 - 172: 32.356 distance: 96 - 169: 35.158 distance: 139 - 143: 31.176 distance: 143 - 144: 4.383 distance: 144 - 145: 68.041 distance: 145 - 146: 40.658 distance: 145 - 154: 69.530 distance: 147 - 148: 70.292 distance: 148 - 150: 39.298 distance: 150 - 152: 55.597 distance: 151 - 153: 54.138 distance: 152 - 153: 21.163 distance: 154 - 155: 38.806 distance: 154 - 160: 39.887 distance: 155 - 156: 39.577 distance: 155 - 158: 40.863 distance: 156 - 157: 39.893 distance: 156 - 161: 40.060 distance: 159 - 160: 40.819 distance: 161 - 162: 56.300 distance: 163 - 164: 40.675 distance: 163 - 169: 40.469 distance: 165 - 166: 40.791 distance: 166 - 167: 40.638 distance: 166 - 168: 56.013 distance: 169 - 170: 55.350 distance: 170 - 171: 41.285 distance: 171 - 172: 39.755 distance: 171 - 174: 39.833 distance: 174 - 175: 40.519 distance: 175 - 176: 14.392 distance: 176 - 177: 58.844 distance: 176 - 180: 48.396 distance: 178 - 179: 40.751 distance: 180 - 181: 60.912 distance: 181 - 182: 48.006 distance: 181 - 184: 41.817 distance: 182 - 192: 40.115 distance: 185 - 186: 56.996 distance: 186 - 188: 55.339 distance: 188 - 190: 41.050 distance: 189 - 190: 39.273 distance: 190 - 191: 68.832 distance: 192 - 193: 39.492 distance: 193 - 194: 40.269 distance: 193 - 196: 68.986 distance: 194 - 195: 39.312 distance: 194 - 198: 41.104 distance: 198 - 199: 38.587 distance: 199 - 200: 38.498 distance: 200 - 201: 56.403 distance: 200 - 209: 41.276 distance: 202 - 203: 57.772 distance: 203 - 204: 9.669 distance: 203 - 205: 9.874 distance: 204 - 206: 36.162 distance: 206 - 208: 53.265 distance: 207 - 208: 39.114 distance: 210 - 211: 55.921 distance: 210 - 213: 56.496 distance: 211 - 212: 39.447 distance: 214 - 215: 67.765 distance: 215 - 216: 56.563 distance: 216 - 217: 37.235 distance: 217 - 218: 55.239 distance: 217 - 219: 53.809 distance: 220 - 221: 38.586 distance: 220 - 226: 56.183 distance: 221 - 222: 40.997 distance: 221 - 224: 56.219 distance: 222 - 227: 33.837 distance: 224 - 225: 40.882 distance: 225 - 226: 57.441