Starting phenix.real_space_refine on Wed Jul 23 23:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.map" model { file = "/net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jt1_61788/07_2025/9jt1_61788.cif" } resolution = 3.09 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= 0.003 sd= 0.168 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 41 5.16 5 C 2908 2.51 5 N 763 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4589 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 96} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 561 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 547 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.42, per 1000 atoms: 0.75 Number of scatterers: 4589 At special positions: 0 Unit cell: (67.221, 99.231, 86.427, 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 41 16.00 O 877 8.00 N 763 7.00 C 2908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 137 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " 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 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 573.2 milliseconds 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 14.9% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.676A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG H 30 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.561A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.650A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.539A pdb=" N ASN L 29 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.863A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.072A pdb=" N THR C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 156 through 168 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.206A pdb=" N TYR H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.615A pdb=" N VAL H 108 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.716A pdb=" N VAL L 10 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.716A pdb=" N VAL L 10 " --> pdb=" O ARG L 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.288A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.288A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.649A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.791A pdb=" N ILE D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB4, first strand: chain 'B' and resid 125 through 126 removed outlier: 4.410A pdb=" N MET B 125 " --> pdb=" O TYR B 134 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1439 1.34 - 1.46: 1159 1.46 - 1.58: 2048 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4699 Sorted by residual: bond pdb=" N GLY C 100 " pdb=" CA GLY C 100 " ideal model delta sigma weight residual 1.449 1.465 -0.015 1.45e-02 4.76e+03 1.12e+00 bond pdb=" C TYR L 48 " pdb=" N GLU L 49 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 7.99e-01 bond pdb=" CB ILE L 47 " pdb=" CG2 ILE L 47 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.77e-01 bond pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 5.04e-01 bond pdb=" CB PRO D 95 " pdb=" CG PRO D 95 " ideal model delta sigma weight residual 1.506 1.479 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 4694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 5848 0.87 - 1.74: 441 1.74 - 2.60: 70 2.60 - 3.47: 32 3.47 - 4.34: 6 Bond angle restraints: 6397 Sorted by residual: angle pdb=" N VAL L 46 " pdb=" CA VAL L 46 " pdb=" C VAL L 46 " ideal model delta sigma weight residual 111.81 109.04 2.77 8.60e-01 1.35e+00 1.04e+01 angle pdb=" N VAL H 61 " pdb=" CA VAL H 61 " pdb=" C VAL H 61 " ideal model delta sigma weight residual 110.05 107.40 2.65 1.09e+00 8.42e-01 5.91e+00 angle pdb=" C SER D 50 " pdb=" N THR D 51 " pdb=" CA THR D 51 " ideal model delta sigma weight residual 121.54 125.78 -4.24 1.91e+00 2.74e-01 4.93e+00 angle pdb=" N SER D 65 " pdb=" CA SER D 65 " pdb=" C SER D 65 " ideal model delta sigma weight residual 108.24 110.92 -2.68 1.32e+00 5.74e-01 4.13e+00 angle pdb=" C CYS B 149 " pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 123.04 121.33 1.71 9.20e-01 1.18e+00 3.45e+00 ... (remaining 6392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.67: 2558 13.67 - 27.35: 155 27.35 - 41.02: 40 41.02 - 54.69: 15 54.69 - 68.36: 5 Dihedral angle restraints: 2773 sinusoidal: 1044 harmonic: 1729 Sorted by residual: dihedral pdb=" CB CYS A 124 " pdb=" SG CYS A 124 " pdb=" SG CYS B 147 " pdb=" CB CYS B 147 " ideal model delta sinusoidal sigma weight residual 93.00 149.38 -56.38 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 106 " pdb=" C VAL A 106 " pdb=" N CYS A 107 " pdb=" CA CYS A 107 " ideal model delta harmonic sigma weight residual 180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 413 0.027 - 0.054: 215 0.054 - 0.081: 40 0.081 - 0.108: 36 0.108 - 0.135: 16 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 717 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO C 14 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO L 14 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 53 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO L 54 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO L 54 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 54 " 0.015 5.00e-02 4.00e+02 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 432 2.75 - 3.28: 4414 3.28 - 3.82: 7826 3.82 - 4.36: 9499 4.36 - 4.90: 16648 Nonbonded interactions: 38819 Sorted by model distance: nonbonded pdb=" OG SER C 52 " pdb=" OD1 ASP C 106 " model vdw 2.207 3.040 nonbonded pdb=" OG SER D 65 " pdb=" OG1 THR D 72 " model vdw 2.219 3.040 nonbonded pdb=" OG SER C 52 " pdb=" OH TYR C 111 " model vdw 2.235 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 89 " model vdw 2.242 3.040 ... (remaining 38814 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 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 or (resid 93 and (name N or name CA or name C or nam \ e O or name CB )) or resid 94 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 143 or (resid 144 and (nam \ e N or name CA or name C or name O or name CB )) or resid 145 through 168)) selection = (chain 'B' and (resid 88 through 126 or resid 133 through 168)) } 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 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: 1.560 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4711 Z= 0.149 Angle : 0.545 4.340 6421 Z= 0.323 Chirality : 0.040 0.135 720 Planarity : 0.003 0.029 802 Dihedral : 10.522 68.363 1635 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 6.15 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.26 (0.36), residues: 593 helix: 2.07 (0.71), residues: 56 sheet: -0.77 (0.37), residues: 193 loop : -0.07 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 PHE 0.013 0.001 PHE H 29 TYR 0.013 0.001 TYR L 48 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.15490 ( 175) hydrogen bonds : angle 8.12209 ( 498) SS BOND : bond 0.00319 ( 12) SS BOND : angle 0.98387 ( 24) covalent geometry : bond 0.00313 ( 4699) covalent geometry : angle 0.54279 ( 6397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7314 (ttm170) REVERT: H 87 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6512 (mtm-85) REVERT: L 102 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7490 (tpt170) REVERT: C 19 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7410 (ttp80) REVERT: C 65 LYS cc_start: 0.7009 (tttp) cc_final: 0.6688 (tttm) REVERT: C 82 GLN cc_start: 0.6663 (tp40) cc_final: 0.6279 (tp40) REVERT: C 85 SER cc_start: 0.7888 (m) cc_final: 0.7278 (t) REVERT: D 42 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7675 (mttt) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.2086 time to fit residues: 29.0932 Evaluate side-chains 93 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111132 restraints weight = 5223.494| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.16 r_work: 0.3031 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4711 Z= 0.134 Angle : 0.518 6.107 6421 Z= 0.271 Chirality : 0.042 0.139 720 Planarity : 0.004 0.029 802 Dihedral : 6.141 50.202 661 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.56 % Allowed : 11.51 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.03 (0.36), residues: 593 helix: 2.40 (0.71), residues: 56 sheet: -0.41 (0.39), residues: 187 loop : -0.11 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 PHE 0.019 0.001 PHE H 29 TYR 0.011 0.001 TYR L 48 ARG 0.003 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 175) hydrogen bonds : angle 5.71245 ( 498) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.37632 ( 24) covalent geometry : bond 0.00319 ( 4699) covalent geometry : angle 0.51199 ( 6397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (mt) REVERT: L 60 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8368 (mtm110) REVERT: L 102 ARG cc_start: 0.8397 (ttt180) cc_final: 0.7916 (tpt170) REVERT: C 65 LYS cc_start: 0.7761 (tttp) cc_final: 0.7483 (tttm) REVERT: C 82 GLN cc_start: 0.8003 (tp40) cc_final: 0.7667 (tp40) REVERT: C 85 SER cc_start: 0.8232 (m) cc_final: 0.7833 (p) REVERT: D 42 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7862 (mttt) REVERT: D 87 TYR cc_start: 0.8878 (m-80) cc_final: 0.8528 (m-80) REVERT: A 141 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7522 (tptm) outliers start: 23 outliers final: 14 residues processed: 105 average time/residue: 0.2019 time to fit residues: 26.1420 Evaluate side-chains 101 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 36 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110793 restraints weight = 5223.374| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.09 r_work: 0.3048 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4711 Z= 0.145 Angle : 0.518 5.778 6421 Z= 0.268 Chirality : 0.041 0.140 720 Planarity : 0.004 0.029 802 Dihedral : 5.311 51.547 655 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.95 % Allowed : 11.11 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.07 (0.36), residues: 593 helix: 2.50 (0.71), residues: 56 sheet: -0.40 (0.38), residues: 191 loop : -0.19 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.002 HIS L 37 PHE 0.018 0.002 PHE H 29 TYR 0.013 0.001 TYR L 48 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.02573 ( 175) hydrogen bonds : angle 5.45172 ( 498) SS BOND : bond 0.00457 ( 12) SS BOND : angle 1.14218 ( 24) covalent geometry : bond 0.00349 ( 4699) covalent geometry : angle 0.51420 ( 6397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8414 (ttt180) cc_final: 0.7929 (tpt170) REVERT: C 13 LYS cc_start: 0.8349 (tppt) cc_final: 0.7972 (tptt) REVERT: C 65 LYS cc_start: 0.7759 (tttp) cc_final: 0.7486 (tttm) REVERT: C 82 GLN cc_start: 0.8092 (tp40) cc_final: 0.7621 (tp40) REVERT: C 83 MET cc_start: 0.8659 (mtp) cc_final: 0.8423 (mtp) REVERT: C 85 SER cc_start: 0.8203 (m) cc_final: 0.7616 (t) REVERT: D 42 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7841 (mttt) REVERT: D 87 TYR cc_start: 0.8869 (m-80) cc_final: 0.8549 (m-80) REVERT: A 141 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7555 (pttt) outliers start: 30 outliers final: 23 residues processed: 103 average time/residue: 0.2107 time to fit residues: 26.7974 Evaluate side-chains 105 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 1 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.135556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111183 restraints weight = 5282.399| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.07 r_work: 0.3191 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4711 Z= 0.142 Angle : 0.521 5.959 6421 Z= 0.267 Chirality : 0.041 0.142 720 Planarity : 0.003 0.029 802 Dihedral : 5.305 53.349 654 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.16 % Allowed : 12.70 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.08 (0.36), residues: 593 helix: 2.62 (0.71), residues: 56 sheet: -0.35 (0.38), residues: 191 loop : -0.25 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 PHE 0.016 0.001 PHE H 29 TYR 0.013 0.001 TYR L 48 ARG 0.003 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.02449 ( 175) hydrogen bonds : angle 5.29638 ( 498) SS BOND : bond 0.00454 ( 12) SS BOND : angle 1.34772 ( 24) covalent geometry : bond 0.00340 ( 4699) covalent geometry : angle 0.51512 ( 6397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8393 (ttt180) cc_final: 0.7957 (tpt170) REVERT: C 13 LYS cc_start: 0.8364 (tppt) cc_final: 0.7949 (tptt) REVERT: C 82 GLN cc_start: 0.8108 (tp40) cc_final: 0.7758 (tp40) REVERT: C 83 MET cc_start: 0.8590 (mtp) cc_final: 0.8278 (mtp) REVERT: C 85 SER cc_start: 0.8218 (m) cc_final: 0.7666 (t) REVERT: D 42 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7837 (mttt) REVERT: D 87 TYR cc_start: 0.8841 (m-80) cc_final: 0.8566 (m-80) REVERT: A 141 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7621 (pttt) outliers start: 26 outliers final: 20 residues processed: 92 average time/residue: 0.2056 time to fit residues: 23.3752 Evaluate side-chains 101 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 55 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.137736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113742 restraints weight = 5302.163| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.06 r_work: 0.3117 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4711 Z= 0.107 Angle : 0.489 5.848 6421 Z= 0.249 Chirality : 0.040 0.142 720 Planarity : 0.003 0.029 802 Dihedral : 5.227 54.074 654 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.36 % Allowed : 13.29 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.03 (0.36), residues: 593 helix: 2.73 (0.71), residues: 56 sheet: -0.20 (0.38), residues: 190 loop : -0.24 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 PHE 0.013 0.001 PHE H 29 TYR 0.012 0.001 TYR L 48 ARG 0.002 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.02217 ( 175) hydrogen bonds : angle 5.06091 ( 498) SS BOND : bond 0.00359 ( 12) SS BOND : angle 0.95235 ( 24) covalent geometry : bond 0.00257 ( 4699) covalent geometry : angle 0.48671 ( 6397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7737 (tpt170) REVERT: C 13 LYS cc_start: 0.8304 (tppt) cc_final: 0.7867 (tptt) REVERT: C 82 GLN cc_start: 0.8031 (tp40) cc_final: 0.7390 (tp40) REVERT: C 85 SER cc_start: 0.8138 (m) cc_final: 0.7558 (t) REVERT: D 42 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7725 (mttt) REVERT: D 87 TYR cc_start: 0.8790 (m-80) cc_final: 0.8516 (m-80) REVERT: A 141 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7576 (pttt) outliers start: 27 outliers final: 21 residues processed: 99 average time/residue: 0.1922 time to fit residues: 23.5970 Evaluate side-chains 101 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.136017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110886 restraints weight = 5259.256| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.18 r_work: 0.3131 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4711 Z= 0.164 Angle : 0.528 6.523 6421 Z= 0.270 Chirality : 0.042 0.144 720 Planarity : 0.003 0.028 802 Dihedral : 5.455 58.137 654 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.75 % Allowed : 14.88 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.07 (0.36), residues: 593 helix: 2.68 (0.72), residues: 56 sheet: -0.30 (0.37), residues: 202 loop : -0.09 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.003 0.002 HIS L 37 PHE 0.017 0.001 PHE H 29 TYR 0.015 0.001 TYR L 48 ARG 0.003 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.02447 ( 175) hydrogen bonds : angle 5.18402 ( 498) SS BOND : bond 0.00563 ( 12) SS BOND : angle 1.22799 ( 24) covalent geometry : bond 0.00395 ( 4699) covalent geometry : angle 0.52397 ( 6397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8332 (ttt180) cc_final: 0.7900 (tpt170) REVERT: C 13 LYS cc_start: 0.8316 (tppt) cc_final: 0.7879 (tptt) REVERT: C 82 GLN cc_start: 0.8143 (tp40) cc_final: 0.7534 (tp40) REVERT: C 85 SER cc_start: 0.8343 (m) cc_final: 0.7783 (t) REVERT: A 141 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7664 (pttt) REVERT: A 164 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8809 (mm-30) outliers start: 29 outliers final: 25 residues processed: 100 average time/residue: 0.2108 time to fit residues: 25.5703 Evaluate side-chains 109 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.134777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110427 restraints weight = 5267.354| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.07 r_work: 0.3051 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4711 Z= 0.144 Angle : 0.507 5.986 6421 Z= 0.260 Chirality : 0.041 0.142 720 Planarity : 0.003 0.029 802 Dihedral : 5.461 58.404 654 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.56 % Allowed : 15.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.08 (0.36), residues: 593 helix: 2.72 (0.72), residues: 56 sheet: -0.24 (0.38), residues: 202 loop : -0.13 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 PHE 0.016 0.001 PHE H 29 TYR 0.013 0.001 TYR L 48 ARG 0.003 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.02334 ( 175) hydrogen bonds : angle 5.12202 ( 498) SS BOND : bond 0.00491 ( 12) SS BOND : angle 1.06734 ( 24) covalent geometry : bond 0.00345 ( 4699) covalent geometry : angle 0.50361 ( 6397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7484 (tpt170) REVERT: C 13 LYS cc_start: 0.8296 (tppt) cc_final: 0.7940 (tppt) REVERT: C 82 GLN cc_start: 0.7847 (tp40) cc_final: 0.7125 (tp40) REVERT: C 85 SER cc_start: 0.8115 (m) cc_final: 0.7512 (t) REVERT: A 141 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7259 (pttt) REVERT: A 164 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8667 (mm-30) outliers start: 28 outliers final: 26 residues processed: 96 average time/residue: 0.2019 time to fit residues: 23.8715 Evaluate side-chains 106 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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: 59.1612 > 50: distance: 11 - 97: 22.245 distance: 21 - 77: 15.927 distance: 24 - 74: 5.185 distance: 34 - 37: 6.341 distance: 37 - 38: 7.330 distance: 38 - 39: 3.066 distance: 38 - 41: 12.865 distance: 39 - 40: 11.502 distance: 39 - 42: 9.214 distance: 42 - 43: 9.729 distance: 42 - 48: 12.704 distance: 43 - 44: 12.621 distance: 43 - 46: 7.317 distance: 44 - 45: 6.314 distance: 44 - 49: 3.128 distance: 46 - 47: 13.431 distance: 47 - 48: 18.469 distance: 49 - 50: 27.512 distance: 50 - 51: 20.021 distance: 51 - 52: 15.290 distance: 51 - 53: 14.486 distance: 53 - 54: 5.981 distance: 54 - 55: 8.900 distance: 55 - 56: 9.071 distance: 55 - 62: 12.324 distance: 57 - 58: 12.530 distance: 58 - 59: 8.355 distance: 59 - 60: 5.099 distance: 60 - 61: 4.271 distance: 62 - 63: 8.549 distance: 63 - 64: 5.953 distance: 64 - 65: 20.154 distance: 64 - 66: 8.699 distance: 66 - 67: 3.836 distance: 67 - 68: 5.237 distance: 67 - 70: 5.569 distance: 68 - 69: 10.385 distance: 68 - 74: 6.881 distance: 70 - 71: 7.998 distance: 71 - 72: 8.447 distance: 71 - 73: 20.050 distance: 74 - 75: 4.218 distance: 75 - 76: 5.427 distance: 75 - 78: 5.369 distance: 76 - 77: 18.957 distance: 76 - 83: 3.213 distance: 78 - 79: 7.029 distance: 79 - 80: 9.077 distance: 80 - 81: 8.105 distance: 80 - 82: 8.270 distance: 83 - 84: 25.601 distance: 84 - 85: 31.940 distance: 84 - 87: 22.833 distance: 85 - 86: 8.220 distance: 85 - 97: 7.788 distance: 87 - 88: 7.433 distance: 88 - 89: 7.542 distance: 88 - 90: 10.021 distance: 89 - 91: 7.493 distance: 90 - 92: 3.117 distance: 90 - 93: 11.291 distance: 91 - 92: 11.254 distance: 92 - 94: 11.689 distance: 93 - 95: 10.359 distance: 94 - 96: 8.709 distance: 95 - 96: 3.862 distance: 97 - 98: 11.345 distance: 98 - 99: 12.168 distance: 98 - 101: 33.337 distance: 99 - 100: 17.907 distance: 99 - 104: 12.088 distance: 101 - 102: 9.158 distance: 101 - 103: 27.788 distance: 104 - 105: 12.596 distance: 105 - 108: 16.934 distance: 106 - 107: 15.185 distance: 106 - 109: 7.007