Starting phenix.real_space_refine on Sat Apr 26 21:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/04_2025/7wsc_32753.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 15 5.16 5 C 2156 2.51 5 N 563 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 3369 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.51, per 1000 atoms: 1.04 Number of scatterers: 3369 At special positions: 0 Unit cell: (63.13, 87.74, 74.9, 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 15 16.00 O 635 8.00 N 563 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.01 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 388.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 364 through 369 removed outlier: 3.593A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 4.117A pdb=" N ASN R 388 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.870A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O VAL H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'L' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.915A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.861A pdb=" N LEU H 37 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70 removed outlier: 6.433A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 144 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.736A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.554A pdb=" N ILE L 109 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 532 1.26 - 1.40: 979 1.40 - 1.54: 1912 1.54 - 1.68: 17 1.68 - 1.82: 18 Bond restraints: 3458 Sorted by residual: bond pdb=" CA TYR R 380 " pdb=" C TYR R 380 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.35e-02 5.49e+03 9.08e+01 bond pdb=" C PHE R 377 " pdb=" O PHE R 377 " ideal model delta sigma weight residual 1.235 1.116 0.120 1.26e-02 6.30e+03 9.01e+01 bond pdb=" C VAL R 382 " pdb=" O VAL R 382 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.03e-02 9.43e+03 6.47e+01 bond pdb=" CB TYR R 380 " pdb=" CG TYR R 380 " ideal model delta sigma weight residual 1.512 1.341 0.171 2.20e-02 2.07e+03 6.07e+01 bond pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 1.523 1.436 0.088 1.25e-02 6.40e+03 4.91e+01 ... (remaining 3453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 4634 6.03 - 12.06: 48 12.06 - 18.09: 10 18.09 - 24.12: 1 24.12 - 30.15: 2 Bond angle restraints: 4695 Sorted by residual: angle pdb=" N GLY R 482 " pdb=" CA GLY R 482 " pdb=" C GLY R 482 " ideal model delta sigma weight residual 113.18 85.51 27.67 2.37e+00 1.78e-01 1.36e+02 angle pdb=" C PHE R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.84 132.96 -13.12 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N PHE R 486 " pdb=" CA PHE R 486 " pdb=" C PHE R 486 " ideal model delta sigma weight residual 111.04 95.20 15.84 1.55e+00 4.16e-01 1.04e+02 angle pdb=" N ALA R 475 " pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 107.98 89.55 18.43 1.88e+00 2.83e-01 9.61e+01 angle pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" CD PRO L 37 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 4690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1778 15.87 - 31.73: 183 31.73 - 47.60: 60 47.60 - 63.46: 15 63.46 - 79.32: 8 Dihedral angle restraints: 2044 sinusoidal: 827 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.68 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N CYS R 488 " pdb=" C CYS R 488 " pdb=" CA CYS R 488 " pdb=" CB CYS R 488 " ideal model delta harmonic sigma weight residual 122.80 106.51 16.29 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ARG H 71 " pdb=" C ARG H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 2041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 476 0.158 - 0.317: 11 0.317 - 0.475: 6 0.475 - 0.633: 4 0.633 - 0.791: 2 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA CYS R 379 " pdb=" N CYS R 379 " pdb=" C CYS R 379 " pdb=" CB CYS R 379 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN R 477 " pdb=" N ASN R 477 " pdb=" C ASN R 477 " pdb=" CB ASN R 477 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 496 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.119 5.00e-02 4.00e+02 1.69e-01 4.60e+01 pdb=" N PRO R 491 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 368 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU R 368 " 0.111 2.00e-02 2.50e+03 pdb=" O LEU R 368 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR R 369 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 477 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASN R 477 " -0.110 2.00e-02 2.50e+03 pdb=" O ASN R 477 " 0.043 2.00e-02 2.50e+03 pdb=" N LYS R 478 " 0.035 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 1670 2.92 - 3.58: 4936 3.58 - 4.24: 7946 4.24 - 4.90: 13267 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" O TYR R 473 " pdb=" O CYS R 488 " model vdw 1.600 3.040 nonbonded pdb=" OG1 THR L 33 " pdb=" OE2 GLU L 36 " model vdw 2.071 3.040 nonbonded pdb=" O ASN R 477 " pdb=" ND2 ASN R 477 " model vdw 2.084 3.120 nonbonded pdb=" OG SER H 36 " pdb=" O MET H 102 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.118 3.040 ... (remaining 27823 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.171 3465 Z= 0.744 Angle : 1.675 30.153 4711 Z= 0.883 Chirality : 0.101 0.791 499 Planarity : 0.012 0.169 604 Dihedral : 15.341 79.299 1263 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 41.09 Ramachandran Plot: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.64 % Rotamer: Outliers : 4.99 % Allowed : 1.94 % Favored : 93.07 % Cbeta Deviations : 1.31 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.39), residues: 414 helix: -5.03 (0.30), residues: 12 sheet: -2.57 (0.41), residues: 129 loop : -2.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 PHE 0.056 0.004 PHE R 490 TYR 0.023 0.002 TYR H 51 ARG 0.039 0.002 ARG R 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 0.76176 ( 3) link_BETA1-4 : bond 0.00848 ( 1) link_BETA1-4 : angle 0.61650 ( 3) hydrogen bonds : bond 0.26234 ( 74) hydrogen bonds : angle 12.54557 ( 183) SS BOND : bond 0.01209 ( 5) SS BOND : angle 4.15259 ( 10) covalent geometry : bond 0.01274 ( 3458) covalent geometry : angle 1.66708 ( 4695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.415 Fit side-chains REVERT: R 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 423 TYR cc_start: 0.7992 (t80) cc_final: 0.7695 (t80) REVERT: R 455 LEU cc_start: 0.7505 (pt) cc_final: 0.7293 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6242 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7557 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7213 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7826 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.1601 time to fit residues: 25.5331 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 474 GLN Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 486 PHE Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain L residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115312 restraints weight = 5825.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119304 restraints weight = 3388.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122043 restraints weight = 2336.119| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 3465 Z= 0.266 Angle : 0.997 13.883 4711 Z= 0.494 Chirality : 0.056 0.373 499 Planarity : 0.010 0.149 604 Dihedral : 10.162 86.175 542 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.80 % Favored : 86.47 % Rotamer: Outliers : 6.37 % Allowed : 14.40 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.39), residues: 414 helix: -3.30 (1.06), residues: 12 sheet: -2.49 (0.40), residues: 128 loop : -2.46 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 59 HIS 0.009 0.003 HIS H 54 PHE 0.025 0.003 PHE R 486 TYR 0.023 0.002 TYR H 51 ARG 0.009 0.001 ARG H 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 1) link_NAG-ASN : angle 0.90979 ( 3) link_BETA1-4 : bond 0.00562 ( 1) link_BETA1-4 : angle 1.14111 ( 3) hydrogen bonds : bond 0.04498 ( 74) hydrogen bonds : angle 8.95896 ( 183) SS BOND : bond 0.00391 ( 5) SS BOND : angle 2.46124 ( 10) covalent geometry : bond 0.00629 ( 3458) covalent geometry : angle 0.99115 ( 4695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6056 (p90) REVERT: R 377 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: R 423 TYR cc_start: 0.8188 (t80) cc_final: 0.7878 (t80) REVERT: R 472 ILE cc_start: 0.3328 (OUTLIER) cc_final: 0.3094 (mm) REVERT: L 26 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6670 (p) REVERT: L 28 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7214 (tt) REVERT: L 50 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7278 (tm-30) REVERT: L 111 TYR cc_start: 0.8453 (m-80) cc_final: 0.7703 (m-80) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 0.1509 time to fit residues: 21.3962 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 358 ILE Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 488 CYS Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** 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 = 0.3874 r_free = 0.3874 target = 0.141744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117544 restraints weight = 5680.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121628 restraints weight = 3295.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124518 restraints weight = 2268.705| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 3465 Z= 0.185 Angle : 0.862 13.533 4711 Z= 0.431 Chirality : 0.051 0.182 499 Planarity : 0.008 0.139 604 Dihedral : 8.346 58.764 534 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 6.65 % Allowed : 17.73 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.40), residues: 414 helix: -3.32 (0.99), residues: 12 sheet: -2.48 (0.41), residues: 130 loop : -2.06 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 59 HIS 0.005 0.002 HIS H 54 PHE 0.014 0.002 PHE H 48 TYR 0.019 0.002 TYR H 51 ARG 0.006 0.001 ARG H 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.02070 ( 3) link_BETA1-4 : bond 0.00627 ( 1) link_BETA1-4 : angle 1.12642 ( 3) hydrogen bonds : bond 0.03827 ( 74) hydrogen bonds : angle 8.31834 ( 183) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.67804 ( 10) covalent geometry : bond 0.00447 ( 3458) covalent geometry : angle 0.85881 ( 4695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: R 423 TYR cc_start: 0.8095 (t80) cc_final: 0.7737 (t80) REVERT: H 72 TYR cc_start: 0.7100 (p90) cc_final: 0.6651 (p90) REVERT: H 134 TYR cc_start: 0.8738 (p90) cc_final: 0.8043 (p90) REVERT: L 28 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7171 (tt) REVERT: L 42 CYS cc_start: 0.6196 (m) cc_final: 0.5933 (m) REVERT: L 50 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7325 (tm-30) REVERT: L 52 ASN cc_start: 0.8552 (p0) cc_final: 0.8077 (p0) REVERT: L 62 GLN cc_start: 0.8751 (pt0) cc_final: 0.8518 (pt0) REVERT: L 74 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8413 (tt) REVERT: L 111 TYR cc_start: 0.8253 (m-80) cc_final: 0.7665 (m-80) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.1447 time to fit residues: 22.0657 Evaluate side-chains 118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN L 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117400 restraints weight = 5818.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121593 restraints weight = 3307.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124428 restraints weight = 2241.959| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 3465 Z= 0.196 Angle : 0.833 13.845 4711 Z= 0.414 Chirality : 0.049 0.168 499 Planarity : 0.007 0.133 604 Dihedral : 7.811 55.244 527 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.35 % Favored : 88.16 % Rotamer: Outliers : 6.93 % Allowed : 20.22 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.41), residues: 414 helix: -3.32 (1.00), residues: 12 sheet: -2.45 (0.41), residues: 130 loop : -1.88 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.012 0.002 PHE H 48 TYR 0.013 0.001 TYR H 51 ARG 0.005 0.001 ARG H 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.00133 ( 3) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 1.00180 ( 3) hydrogen bonds : bond 0.03745 ( 74) hydrogen bonds : angle 7.87455 ( 183) SS BOND : bond 0.00277 ( 5) SS BOND : angle 1.68958 ( 10) covalent geometry : bond 0.00474 ( 3458) covalent geometry : angle 0.82967 ( 4695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: R 423 TYR cc_start: 0.8112 (t80) cc_final: 0.7797 (t80) REVERT: H 72 TYR cc_start: 0.7124 (p90) cc_final: 0.6645 (p90) REVERT: L 28 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7413 (tt) REVERT: L 62 GLN cc_start: 0.8705 (pt0) cc_final: 0.8013 (pt0) REVERT: L 74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8450 (tt) REVERT: L 111 TYR cc_start: 0.8278 (m-80) cc_final: 0.7709 (m-80) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.1340 time to fit residues: 19.8494 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN H 103 ASN ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119312 restraints weight = 5756.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123525 restraints weight = 3236.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126479 restraints weight = 2189.613| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3465 Z= 0.166 Angle : 0.818 13.855 4711 Z= 0.403 Chirality : 0.048 0.166 499 Planarity : 0.007 0.128 604 Dihedral : 7.510 51.179 527 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.14 % Favored : 89.37 % Rotamer: Outliers : 6.37 % Allowed : 22.44 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.42), residues: 414 helix: -3.14 (1.04), residues: 12 sheet: -2.41 (0.42), residues: 131 loop : -1.73 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.015 0.002 PHE H 133 TYR 0.020 0.002 TYR L 56 ARG 0.006 0.001 ARG H 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 0.97277 ( 3) link_BETA1-4 : bond 0.00517 ( 1) link_BETA1-4 : angle 1.02073 ( 3) hydrogen bonds : bond 0.03575 ( 74) hydrogen bonds : angle 7.62283 ( 183) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.69494 ( 10) covalent geometry : bond 0.00402 ( 3458) covalent geometry : angle 0.81447 ( 4695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8034 (t80) cc_final: 0.7699 (t80) REVERT: R 489 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6974 (t80) REVERT: H 32 GLN cc_start: 0.7185 (tp-100) cc_final: 0.6947 (mm-40) REVERT: H 72 TYR cc_start: 0.7162 (p90) cc_final: 0.6648 (p90) REVERT: H 123 TYR cc_start: 0.8675 (p90) cc_final: 0.8347 (p90) REVERT: L 50 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7472 (tm-30) REVERT: L 62 GLN cc_start: 0.8608 (pt0) cc_final: 0.7977 (pt0) REVERT: L 74 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8420 (tt) REVERT: L 111 TYR cc_start: 0.8289 (m-80) cc_final: 0.7693 (m-80) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.1571 time to fit residues: 21.5570 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.142869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118575 restraints weight = 5889.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122848 restraints weight = 3363.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125803 restraints weight = 2268.887| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 3465 Z= 0.182 Angle : 0.817 13.998 4711 Z= 0.401 Chirality : 0.047 0.167 499 Planarity : 0.007 0.124 604 Dihedral : 7.057 48.585 525 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.11 % Favored : 88.41 % Rotamer: Outliers : 6.93 % Allowed : 23.55 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.41), residues: 414 helix: -3.67 (0.70), residues: 18 sheet: -2.21 (0.44), residues: 124 loop : -1.72 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.012 0.002 PHE H 87 TYR 0.019 0.001 TYR L 73 ARG 0.007 0.001 ARG H 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 0.96095 ( 3) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 0.98918 ( 3) hydrogen bonds : bond 0.03522 ( 74) hydrogen bonds : angle 7.54830 ( 183) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.59152 ( 10) covalent geometry : bond 0.00439 ( 3458) covalent geometry : angle 0.81394 ( 4695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8015 (t80) cc_final: 0.7772 (t80) REVERT: R 489 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.7086 (t80) REVERT: H 72 TYR cc_start: 0.7211 (p90) cc_final: 0.6686 (p90) REVERT: H 77 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8334 (mmtt) REVERT: H 123 TYR cc_start: 0.8650 (p90) cc_final: 0.8311 (p90) REVERT: L 50 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7559 (tm-30) REVERT: L 62 GLN cc_start: 0.8579 (pt0) cc_final: 0.8068 (pt0) REVERT: L 74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8497 (tt) REVERT: L 111 TYR cc_start: 0.8254 (m-80) cc_final: 0.7691 (m-80) outliers start: 25 outliers final: 19 residues processed: 113 average time/residue: 0.1490 time to fit residues: 20.5460 Evaluate side-chains 115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** 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 = 0.3912 r_free = 0.3912 target = 0.144326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120350 restraints weight = 5780.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124632 restraints weight = 3226.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127614 restraints weight = 2154.886| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3465 Z= 0.152 Angle : 0.796 13.941 4711 Z= 0.393 Chirality : 0.047 0.149 499 Planarity : 0.007 0.121 604 Dihedral : 6.825 47.320 525 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.42 % Favored : 90.10 % Rotamer: Outliers : 7.20 % Allowed : 23.55 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.41), residues: 414 helix: -3.51 (0.76), residues: 18 sheet: -2.29 (0.43), residues: 131 loop : -1.65 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.011 0.002 PHE H 87 TYR 0.019 0.001 TYR L 73 ARG 0.007 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 1) link_NAG-ASN : angle 0.87645 ( 3) link_BETA1-4 : bond 0.00446 ( 1) link_BETA1-4 : angle 0.93521 ( 3) hydrogen bonds : bond 0.03463 ( 74) hydrogen bonds : angle 7.38179 ( 183) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.62683 ( 10) covalent geometry : bond 0.00366 ( 3458) covalent geometry : angle 0.79362 ( 4695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: R 423 TYR cc_start: 0.7995 (t80) cc_final: 0.7651 (t80) REVERT: R 489 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7095 (t80) REVERT: H 72 TYR cc_start: 0.7236 (p90) cc_final: 0.6740 (p90) REVERT: H 77 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8122 (mmtt) REVERT: H 123 TYR cc_start: 0.8612 (p90) cc_final: 0.8338 (p90) REVERT: L 50 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7675 (tm-30) REVERT: L 62 GLN cc_start: 0.8530 (pt0) cc_final: 0.8054 (pt0) REVERT: L 74 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8398 (tt) REVERT: L 106 ASP cc_start: 0.7446 (t0) cc_final: 0.7241 (t0) REVERT: L 111 TYR cc_start: 0.8215 (m-80) cc_final: 0.7638 (m-80) outliers start: 26 outliers final: 17 residues processed: 111 average time/residue: 0.1607 time to fit residues: 21.5324 Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 57.1531 > 50: distance: 8 - 181: 5.513 distance: 11 - 178: 7.553 distance: 102 - 107: 24.263 distance: 107 - 108: 25.159 distance: 108 - 109: 43.228 distance: 108 - 111: 12.851 distance: 109 - 115: 21.293 distance: 111 - 112: 9.651 distance: 111 - 113: 11.342 distance: 112 - 114: 10.220 distance: 115 - 116: 20.073 distance: 115 - 189: 23.645 distance: 116 - 117: 18.501 distance: 116 - 119: 20.956 distance: 117 - 118: 7.462 distance: 117 - 121: 12.926 distance: 118 - 186: 8.088 distance: 119 - 120: 36.271 distance: 121 - 122: 5.700 distance: 122 - 123: 3.415 distance: 122 - 125: 9.274 distance: 123 - 124: 6.953 distance: 123 - 132: 6.354 distance: 125 - 126: 12.029 distance: 126 - 127: 13.554 distance: 127 - 128: 5.355 distance: 128 - 129: 23.334 distance: 129 - 130: 25.816 distance: 129 - 131: 25.447 distance: 132 - 133: 3.337 distance: 132 - 174: 12.297 distance: 133 - 134: 7.185 distance: 133 - 136: 3.875 distance: 134 - 135: 13.713 distance: 134 - 140: 6.126 distance: 135 - 171: 17.926 distance: 137 - 138: 11.466 distance: 137 - 139: 10.741 distance: 140 - 141: 3.005 distance: 141 - 142: 3.065 distance: 141 - 144: 4.136 distance: 142 - 143: 8.344 distance: 142 - 148: 5.872 distance: 145 - 146: 3.320 distance: 148 - 149: 7.003 distance: 149 - 150: 4.486 distance: 149 - 152: 9.820 distance: 150 - 151: 18.315 distance: 150 - 154: 11.394 distance: 152 - 153: 16.373 distance: 155 - 156: 3.488 distance: 155 - 158: 9.345 distance: 156 - 157: 9.323 distance: 156 - 163: 14.683 distance: 158 - 159: 6.176 distance: 159 - 160: 7.747 distance: 160 - 161: 5.769 distance: 161 - 162: 5.278 distance: 163 - 164: 11.097 distance: 164 - 165: 3.880 distance: 164 - 167: 13.056 distance: 165 - 166: 14.403 distance: 165 - 171: 3.567 distance: 167 - 168: 12.005 distance: 168 - 169: 3.631 distance: 168 - 170: 12.109 distance: 171 - 172: 5.870 distance: 172 - 173: 3.575 distance: 172 - 175: 9.455 distance: 173 - 174: 12.245 distance: 175 - 176: 7.411 distance: 175 - 177: 4.654 distance: 178 - 179: 5.197 distance: 179 - 180: 7.401 distance: 179 - 182: 5.221 distance: 180 - 181: 10.569 distance: 180 - 186: 6.290 distance: 182 - 183: 6.909 distance: 183 - 184: 7.455 distance: 183 - 185: 14.991