Starting phenix.real_space_refine on Sat Jun 14 21:29:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.map" model { file = "/net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uw1_42636/06_2025/8uw1_42636.cif" } resolution = 2.88 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= 0.005 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5964 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 13 5.16 5 C 6726 2.51 5 N 2282 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12164 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 745 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 29} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 8.19, per 1000 atoms: 0.67 Number of scatterers: 12164 At special positions: 0 Unit cell: (84.15, 120.7, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 292 15.00 O 2851 8.00 N 2282 7.00 C 6726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 987.2 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 68.7% alpha, 3.1% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.594A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.592A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.588A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.667A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.592A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.517A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.790A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.690A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.770A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.625A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.722A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.540A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.308A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.821A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.300A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 394 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 3.85 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: 2103 1.33 - 1.45: 4333 1.45 - 1.57: 5929 1.57 - 1.69: 582 1.69 - 1.81: 24 Bond restraints: 12971 Sorted by residual: bond pdb=" N ASP K 194 " pdb=" CA ASP K 194 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.30e-02 5.92e+03 6.27e+00 bond pdb=" N TYR K 196 " pdb=" CA TYR K 196 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.22e+00 bond pdb=" N ALA K 192 " pdb=" CA ALA K 192 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.76e+00 bond pdb=" N GLN K 191 " pdb=" CA GLN K 191 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.56e+00 bond pdb=" P DT J 75 " pdb=" OP2 DT J 75 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 12966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18337 2.04 - 4.08: 397 4.08 - 6.12: 32 6.12 - 8.17: 2 8.17 - 10.21: 3 Bond angle restraints: 18771 Sorted by residual: angle pdb=" C3' DA J 73 " pdb=" O3' DA J 73 " pdb=" P DA J 74 " ideal model delta sigma weight residual 120.20 109.99 10.21 1.50e+00 4.44e-01 4.63e+01 angle pdb=" C3' DG J 72 " pdb=" O3' DG J 72 " pdb=" P DA J 73 " ideal model delta sigma weight residual 120.20 110.32 9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" C3' DA J 71 " pdb=" O3' DA J 71 " pdb=" P DG J 72 " ideal model delta sigma weight residual 120.20 110.39 9.81 1.50e+00 4.44e-01 4.28e+01 angle pdb=" C3' DT J 75 " pdb=" O3' DT J 75 " pdb=" P DC J 76 " ideal model delta sigma weight residual 120.20 112.76 7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C3' DA J 74 " pdb=" O3' DA J 74 " pdb=" P DT J 75 " ideal model delta sigma weight residual 120.20 113.36 6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 18766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 5685 35.79 - 71.58: 1359 71.58 - 107.36: 12 107.36 - 143.15: 0 143.15 - 178.94: 2 Dihedral angle restraints: 7058 sinusoidal: 4799 harmonic: 2259 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 38.94 -178.94 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 42.87 177.13 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2053 0.091 - 0.182: 77 0.182 - 0.274: 0 0.274 - 0.365: 0 0.365 - 0.456: 6 Chirality restraints: 2136 Sorted by residual: chirality pdb=" P DA J 71 " pdb=" OP1 DA J 71 " pdb=" OP2 DA J 71 " pdb=" O5' DA J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" P DT J 75 " pdb=" OP1 DT J 75 " pdb=" OP2 DT J 75 " pdb=" O5' DT J 75 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" P DG J 72 " pdb=" OP1 DG J 72 " pdb=" OP2 DG J 72 " pdb=" O5' DG J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 2133 not shown) Planarity restraints: 1370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 141 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.46e+00 pdb=" N9 DA I 141 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 141 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 141 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 141 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 141 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA I 141 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA I 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.026 2.00e-02 2.50e+03 1.10e-02 3.35e+00 pdb=" N9 DA I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.17e+00 pdb=" N9 DA I 39 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.002 2.00e-02 2.50e+03 ... (remaining 1367 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2462 2.80 - 3.32: 9769 3.32 - 3.85: 22246 3.85 - 4.37: 27730 4.37 - 4.90: 38817 Nonbonded interactions: 101024 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.273 3.120 nonbonded pdb=" OE1 GLN E 125 " pdb=" NH1 ARG E 134 " model vdw 2.320 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 181 " model vdw 2.387 3.120 nonbonded pdb=" N VAL C 43 " pdb=" OP1 DA I 113 " model vdw 2.390 3.120 nonbonded pdb=" NH2 ARG C 29 " pdb=" OP1 DC I 123 " model vdw 2.406 3.120 ... (remaining 101019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.008 0.047 12971 Z= 0.333 Angle : 0.726 10.208 18771 Z= 0.444 Chirality : 0.047 0.456 2136 Planarity : 0.004 0.044 1370 Dihedral : 27.266 178.941 5602 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 765 helix: 1.58 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 176 HIS 0.002 0.001 HIS E 113 PHE 0.013 0.002 PHE B 61 TYR 0.022 0.002 TYR G 50 ARG 0.010 0.001 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.12203 ( 764) hydrogen bonds : angle 3.94054 ( 1913) covalent geometry : bond 0.00759 (12971) covalent geometry : angle 0.72622 (18771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7726 (pp20) REVERT: G 73 ASN cc_start: 0.8435 (m110) cc_final: 0.8233 (m110) REVERT: H 45 VAL cc_start: 0.8706 (t) cc_final: 0.8469 (m) REVERT: H 73 GLU cc_start: 0.7923 (tp30) cc_final: 0.7574 (tp30) outliers start: 0 outliers final: 1 residues processed: 111 average time/residue: 1.7041 time to fit residues: 200.5694 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN G 112 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057936 restraints weight = 31868.991| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.52 r_work: 0.2884 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12971 Z= 0.173 Angle : 0.580 5.980 18771 Z= 0.352 Chirality : 0.034 0.130 2136 Planarity : 0.004 0.042 1370 Dihedral : 29.986 178.244 4076 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.09 % Allowed : 10.26 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.30), residues: 765 helix: 2.21 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 176 HIS 0.003 0.001 HIS H 79 PHE 0.011 0.001 PHE H 67 TYR 0.009 0.001 TYR D 37 ARG 0.006 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 764) hydrogen bonds : angle 2.78492 ( 1913) covalent geometry : bond 0.00370 (12971) covalent geometry : angle 0.57959 (18771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.939 Fit side-chains REVERT: B 59 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8574 (tttp) REVERT: C 15 LYS cc_start: 0.7492 (pttp) cc_final: 0.6998 (pptt) REVERT: C 72 ASP cc_start: 0.7506 (m-30) cc_final: 0.7206 (m-30) REVERT: C 90 ASP cc_start: 0.8460 (t70) cc_final: 0.7975 (t0) REVERT: G 36 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8741 (mmtm) outliers start: 7 outliers final: 0 residues processed: 88 average time/residue: 1.7671 time to fit residues: 165.4857 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054752 restraints weight = 31866.013| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.49 r_work: 0.2799 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12971 Z= 0.187 Angle : 0.562 6.812 18771 Z= 0.340 Chirality : 0.034 0.133 2136 Planarity : 0.004 0.036 1370 Dihedral : 30.177 175.502 4074 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.02 % Allowed : 11.82 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.30), residues: 765 helix: 2.38 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.20 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.001 HIS H 79 PHE 0.010 0.001 PHE H 67 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05538 ( 764) hydrogen bonds : angle 2.77372 ( 1913) covalent geometry : bond 0.00417 (12971) covalent geometry : angle 0.56232 (18771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.870 Fit side-chains REVERT: C 72 ASP cc_start: 0.7225 (m-30) cc_final: 0.6938 (m-30) REVERT: C 90 ASP cc_start: 0.8526 (t70) cc_final: 0.8128 (t0) REVERT: D 68 GLU cc_start: 0.8181 (tp30) cc_final: 0.7973 (mt-10) REVERT: E 59 GLU cc_start: 0.8399 (pm20) cc_final: 0.8193 (pm20) REVERT: E 97 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: F 79 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8494 (mttt) REVERT: H 112 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8943 (p) outliers start: 13 outliers final: 2 residues processed: 89 average time/residue: 1.9157 time to fit residues: 180.5539 Evaluate side-chains 80 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056959 restraints weight = 31704.661| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.50 r_work: 0.2858 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12971 Z= 0.147 Angle : 0.513 6.670 18771 Z= 0.315 Chirality : 0.032 0.125 2136 Planarity : 0.003 0.034 1370 Dihedral : 29.961 178.577 4074 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.40 % Allowed : 13.84 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.30), residues: 765 helix: 2.79 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.007 0.001 TYR D 37 ARG 0.003 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 764) hydrogen bonds : angle 2.53982 ( 1913) covalent geometry : bond 0.00309 (12971) covalent geometry : angle 0.51292 (18771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.919 Fit side-chains REVERT: C 72 ASP cc_start: 0.6836 (m-30) cc_final: 0.6532 (m-30) REVERT: C 90 ASP cc_start: 0.8428 (t70) cc_final: 0.8015 (t0) REVERT: D 65 ASP cc_start: 0.9318 (t0) cc_final: 0.9008 (t0) REVERT: E 97 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: F 79 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8555 (mttt) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 1.7877 time to fit residues: 159.2215 Evaluate side-chains 81 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053856 restraints weight = 31610.216| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.48 r_work: 0.2772 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12971 Z= 0.202 Angle : 0.554 7.002 18771 Z= 0.336 Chirality : 0.035 0.133 2136 Planarity : 0.004 0.032 1370 Dihedral : 30.174 179.012 4074 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.56 % Allowed : 13.22 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.30), residues: 765 helix: 2.64 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 176 HIS 0.001 0.001 HIS D 46 PHE 0.008 0.001 PHE B 61 TYR 0.012 0.001 TYR F 51 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.05336 ( 764) hydrogen bonds : angle 2.72339 ( 1913) covalent geometry : bond 0.00457 (12971) covalent geometry : angle 0.55436 (18771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.980 Fit side-chains REVERT: C 72 ASP cc_start: 0.7089 (m-30) cc_final: 0.6766 (m-30) REVERT: C 90 ASP cc_start: 0.8443 (t70) cc_final: 0.8035 (t0) REVERT: D 65 ASP cc_start: 0.9396 (t0) cc_final: 0.9060 (t0) REVERT: E 59 GLU cc_start: 0.8508 (pm20) cc_final: 0.8270 (pm20) REVERT: E 97 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: F 79 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8505 (mptt) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 1.8307 time to fit residues: 159.9404 Evaluate side-chains 83 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054190 restraints weight = 31820.271| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.50 r_work: 0.2779 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12971 Z= 0.166 Angle : 0.542 8.398 18771 Z= 0.330 Chirality : 0.033 0.131 2136 Planarity : 0.004 0.032 1370 Dihedral : 30.157 179.469 4074 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.87 % Allowed : 13.37 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.30), residues: 765 helix: 2.72 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.011 0.001 TYR F 51 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 764) hydrogen bonds : angle 2.69531 ( 1913) covalent geometry : bond 0.00359 (12971) covalent geometry : angle 0.54231 (18771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.350 Fit side-chains REVERT: C 72 ASP cc_start: 0.7004 (m-30) cc_final: 0.6677 (m-30) REVERT: D 65 ASP cc_start: 0.9364 (t0) cc_final: 0.9021 (t0) REVERT: E 97 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: F 79 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8464 (mptt) REVERT: H 112 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8914 (p) outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 1.9114 time to fit residues: 169.1409 Evaluate side-chains 86 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054461 restraints weight = 31793.995| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.49 r_work: 0.2785 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12971 Z= 0.167 Angle : 0.536 6.856 18771 Z= 0.327 Chirality : 0.033 0.131 2136 Planarity : 0.004 0.032 1370 Dihedral : 30.126 179.413 4074 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.87 % Allowed : 13.69 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 765 helix: 2.75 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 PHE 0.009 0.001 PHE E 78 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 764) hydrogen bonds : angle 2.67109 ( 1913) covalent geometry : bond 0.00365 (12971) covalent geometry : angle 0.53636 (18771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.879 Fit side-chains REVERT: C 72 ASP cc_start: 0.6995 (m-30) cc_final: 0.6681 (m-30) REVERT: D 65 ASP cc_start: 0.9385 (t0) cc_final: 0.9061 (t0) REVERT: E 97 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: F 79 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8532 (mttt) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 1.8161 time to fit residues: 156.4032 Evaluate side-chains 84 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054666 restraints weight = 32033.105| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.50 r_work: 0.2792 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12971 Z= 0.163 Angle : 0.536 10.122 18771 Z= 0.326 Chirality : 0.033 0.130 2136 Planarity : 0.004 0.032 1370 Dihedral : 30.110 179.621 4074 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.71 % Allowed : 14.00 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.30), residues: 765 helix: 2.77 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR F 51 ARG 0.003 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 764) hydrogen bonds : angle 2.63217 ( 1913) covalent geometry : bond 0.00356 (12971) covalent geometry : angle 0.53578 (18771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.872 Fit side-chains REVERT: C 72 ASP cc_start: 0.6950 (m-30) cc_final: 0.6626 (m-30) REVERT: D 65 ASP cc_start: 0.9377 (t0) cc_final: 0.9032 (t0) REVERT: E 97 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: F 79 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8534 (mttt) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 1.8559 time to fit residues: 163.3229 Evaluate side-chains 85 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 51.9311 > 50: distance: 96 - 101: 8.581 distance: 101 - 102: 8.068 distance: 101 - 107: 4.531 distance: 102 - 103: 6.820 distance: 102 - 105: 11.515 distance: 103 - 104: 23.828 distance: 103 - 108: 11.020 distance: 105 - 106: 6.447 distance: 106 - 107: 6.535 distance: 108 - 109: 11.560 distance: 109 - 110: 15.575 distance: 109 - 112: 13.519 distance: 110 - 111: 19.995 distance: 110 - 116: 11.888 distance: 112 - 113: 5.457 distance: 113 - 114: 17.772 distance: 114 - 115: 16.407 distance: 116 - 117: 22.716 distance: 116 - 122: 21.465 distance: 117 - 118: 9.858 distance: 117 - 120: 19.857 distance: 118 - 119: 4.479 distance: 118 - 123: 5.811 distance: 120 - 121: 21.875 distance: 121 - 122: 10.980 distance: 123 - 124: 6.214 distance: 124 - 125: 6.925 distance: 124 - 127: 10.877 distance: 125 - 126: 11.502 distance: 125 - 134: 10.258 distance: 127 - 128: 6.573 distance: 128 - 129: 13.601 distance: 129 - 130: 7.175 distance: 130 - 131: 8.309 distance: 134 - 135: 3.246 distance: 135 - 136: 7.852 distance: 135 - 138: 3.612 distance: 136 - 137: 7.317 distance: 136 - 142: 4.940 distance: 138 - 139: 5.510 distance: 139 - 140: 16.514 distance: 139 - 141: 17.367 distance: 142 - 143: 7.453 distance: 143 - 144: 11.234 distance: 143 - 146: 14.591 distance: 144 - 145: 14.871 distance: 144 - 149: 6.226 distance: 146 - 147: 9.123 distance: 146 - 148: 21.568 distance: 149 - 150: 10.927 distance: 150 - 151: 10.452 distance: 150 - 153: 7.968 distance: 151 - 152: 22.112 distance: 151 - 160: 4.184 distance: 153 - 154: 4.180 distance: 154 - 155: 9.565 distance: 154 - 156: 8.701 distance: 155 - 157: 14.319 distance: 156 - 158: 19.914 distance: 157 - 159: 16.046 distance: 158 - 159: 8.888 distance: 160 - 161: 3.322 distance: 161 - 162: 6.381 distance: 161 - 164: 8.436 distance: 162 - 163: 11.853 distance: 162 - 169: 13.024 distance: 164 - 165: 11.672 distance: 165 - 166: 15.179 distance: 166 - 167: 16.882 distance: 166 - 168: 17.488 distance: 169 - 170: 11.463 distance: 170 - 171: 15.778 distance: 170 - 173: 27.127 distance: 171 - 172: 8.234 distance: 171 - 174: 9.505 distance: 174 - 175: 10.257 distance: 175 - 176: 17.992 distance: 176 - 177: 26.125 distance: 176 - 178: 7.179