Starting phenix.real_space_refine on Wed Mar 5 17:09:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovk_17218/03_2025/8ovk_17218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovk_17218/03_2025/8ovk_17218.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/8ovk_17218/03_2025/8ovk_17218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovk_17218/03_2025/8ovk_17218.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovk_17218/03_2025/8ovk_17218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovk_17218/03_2025/8ovk_17218.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= 0.001 sd= 0.009 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 10 5.16 5 C 1940 2.51 5 N 530 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.67, per 1000 atoms: 0.55 Number of scatterers: 3060 At special positions: 0 Unit cell: (100.8, 124.95, 39.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 580 8.00 N 530 7.00 C 1940 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: 0.72 Conformation dependent library (CDL) restraints added in 362.7 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.224A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE C 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 39 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 39 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY E 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 39 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL G 39 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.225A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE D 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 39 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 39 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 39 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE J 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY H 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL H 39 " --> pdb=" O GLY J 38 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.87 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: 1003 1.33 - 1.45: 538 1.45 - 1.57: 1559 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3120 Sorted by residual: bond pdb=" CA GLN D 15 " pdb=" C GLN D 15 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.28e-02 6.10e+03 8.65e+00 bond pdb=" CA GLN B 15 " pdb=" C GLN B 15 " ideal model delta sigma weight residual 1.523 1.485 0.037 1.28e-02 6.10e+03 8.51e+00 bond pdb=" CA GLN I 15 " pdb=" C GLN I 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.45e+00 bond pdb=" CA GLN G 15 " pdb=" C GLN G 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.44e+00 bond pdb=" CA GLN E 15 " pdb=" C GLN E 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.43e+00 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 2778 1.45 - 2.90: 992 2.90 - 4.36: 280 4.36 - 5.81: 90 5.81 - 7.26: 50 Bond angle restraints: 4190 Sorted by residual: angle pdb=" O GLY H 29 " pdb=" C GLY H 29 " pdb=" N ALA H 30 " ideal model delta sigma weight residual 123.59 119.55 4.04 8.70e-01 1.32e+00 2.16e+01 angle pdb=" O GLY E 29 " pdb=" C GLY E 29 " pdb=" N ALA E 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" O GLY C 29 " pdb=" C GLY C 29 " pdb=" N ALA C 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" N PHE D 4 " pdb=" CA PHE D 4 " pdb=" C PHE D 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 angle pdb=" N PHE J 4 " pdb=" CA PHE J 4 " pdb=" C PHE J 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 10.60: 1390 10.60 - 21.18: 193 21.18 - 31.75: 97 31.75 - 42.33: 50 42.33 - 52.90: 20 Dihedral angle restraints: 1750 sinusoidal: 670 harmonic: 1080 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" C LEU J 34 " pdb=" N MET J 35 " pdb=" CA MET J 35 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU G 34 " pdb=" C LEU G 34 " pdb=" N MET G 35 " pdb=" CA MET G 35 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 90 0.046 - 0.092: 141 0.092 - 0.137: 129 0.137 - 0.183: 50 0.183 - 0.229: 30 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA GLU C 11 " pdb=" N GLU C 11 " pdb=" C GLU C 11 " pdb=" CB GLU C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU B 11 " pdb=" N GLU B 11 " pdb=" C GLU B 11 " pdb=" CB GLU B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU G 11 " pdb=" N GLU G 11 " pdb=" C GLU G 11 " pdb=" CB GLU G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 437 not shown) Planarity restraints: 560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.54e+01 pdb=" CG TYR H 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR H 10 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR H 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR D 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 10 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 10 " -0.061 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 10 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 10 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 10 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 10 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 10 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 10 " -0.058 2.00e-02 2.50e+03 ... (remaining 557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1120 2.89 - 3.39: 2591 3.39 - 3.89: 5434 3.89 - 4.40: 6090 4.40 - 4.90: 11642 Nonbonded interactions: 26877 Sorted by model distance: nonbonded pdb=" NH2 ARG H 5 " pdb=" OD2 ASP J 7 " model vdw 2.386 3.120 nonbonded pdb=" NH2 ARG A 5 " pdb=" OD2 ASP C 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG G 5 " pdb=" OD2 ASP I 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG D 5 " pdb=" OD2 ASP F 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG B 5 " pdb=" OD2 ASP D 7 " model vdw 2.387 3.120 ... (remaining 26872 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.012 0.038 3120 Z= 0.812 Angle : 1.803 7.261 4190 Z= 1.167 Chirality : 0.109 0.229 440 Planarity : 0.011 0.036 560 Dihedral : 14.992 52.904 1070 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 12.90 % Allowed : 9.68 % Favored : 77.42 % 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: -1.83 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.027 0.009 PHE B 19 TYR 0.062 0.030 TYR H 10 ARG 0.002 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 5 ARG cc_start: 0.8391 (mtp180) cc_final: 0.6681 (pmt170) REVERT: B 3 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: B 5 ARG cc_start: 0.8356 (mtp180) cc_final: 0.6701 (pmt170) REVERT: C 3 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7026 (mm-30) REVERT: D 3 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: D 28 LYS cc_start: 0.8549 (mttt) cc_final: 0.8026 (mttm) REVERT: E 3 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: E 15 GLN cc_start: 0.8909 (tt0) cc_final: 0.8641 (tt0) REVERT: F 3 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: G 3 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: H 3 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: H 15 GLN cc_start: 0.8933 (tt0) cc_final: 0.8684 (tt0) REVERT: I 3 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: I 5 ARG cc_start: 0.8259 (mtp180) cc_final: 0.6763 (tpm170) REVERT: I 34 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (mt) REVERT: J 3 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: J 5 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7012 (tpm170) outliers start: 40 outliers final: 5 residues processed: 166 average time/residue: 1.1964 time to fit residues: 203.1821 Evaluate side-chains 135 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN F 6 HIS F 15 GLN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097999 restraints weight = 3799.108| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.35 r_work: 0.3564 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3120 Z= 0.212 Angle : 0.528 8.219 4190 Z= 0.283 Chirality : 0.052 0.125 440 Planarity : 0.002 0.011 560 Dihedral : 10.830 59.979 462 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.10 % Allowed : 25.16 % Favored : 67.74 % 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: -2.50 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 14 PHE 0.009 0.001 PHE E 20 TYR 0.007 0.001 TYR G 10 ARG 0.007 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.345 Fit side-chains REVERT: A 3 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: A 5 ARG cc_start: 0.8541 (mtp180) cc_final: 0.6355 (pmt170) REVERT: A 40 VAL cc_start: 0.8811 (m) cc_final: 0.8467 (p) REVERT: B 3 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: B 5 ARG cc_start: 0.8498 (mtp180) cc_final: 0.6256 (pmt170) REVERT: B 22 GLU cc_start: 0.8297 (tt0) cc_final: 0.7697 (tt0) REVERT: B 28 LYS cc_start: 0.8970 (mttm) cc_final: 0.8403 (mttt) REVERT: C 3 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: C 5 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7827 (ttt-90) REVERT: C 22 GLU cc_start: 0.8102 (tt0) cc_final: 0.7840 (tt0) REVERT: D 3 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 28 LYS cc_start: 0.9007 (mttt) cc_final: 0.8738 (mttm) REVERT: E 3 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: E 7 ASP cc_start: 0.8605 (p0) cc_final: 0.8284 (p0) REVERT: E 28 LYS cc_start: 0.8934 (mttt) cc_final: 0.8603 (mttm) REVERT: F 3 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: F 5 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7872 (tpt-90) REVERT: F 28 LYS cc_start: 0.8891 (mttt) cc_final: 0.8623 (mtpt) REVERT: G 3 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: G 5 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7646 (ttt-90) REVERT: G 7 ASP cc_start: 0.8618 (p0) cc_final: 0.8350 (p0) REVERT: G 28 LYS cc_start: 0.9037 (mttt) cc_final: 0.8756 (mttt) REVERT: H 3 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: H 5 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7802 (ttt-90) REVERT: H 7 ASP cc_start: 0.8590 (p0) cc_final: 0.8259 (p0) REVERT: H 28 LYS cc_start: 0.9048 (mttt) cc_final: 0.8671 (mttm) REVERT: I 3 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: I 5 ARG cc_start: 0.7954 (mtp180) cc_final: 0.6640 (tpm170) REVERT: I 28 LYS cc_start: 0.8937 (mttm) cc_final: 0.8590 (mttm) REVERT: J 3 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: J 5 ARG cc_start: 0.8000 (mtp180) cc_final: 0.6650 (tpm170) outliers start: 22 outliers final: 4 residues processed: 122 average time/residue: 1.3155 time to fit residues: 163.9856 Evaluate side-chains 115 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 6 HIS C 14 HIS D 6 HIS D 14 HIS D 15 GLN E 14 HIS F 14 HIS G 6 HIS G 14 HIS H 14 HIS J 6 HIS J 14 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.113568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084774 restraints weight = 3840.709| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.15 r_work: 0.3286 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.065 3120 Z= 0.735 Angle : 0.664 7.877 4190 Z= 0.361 Chirality : 0.056 0.137 440 Planarity : 0.003 0.014 560 Dihedral : 10.350 57.886 450 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 8.71 % Allowed : 23.55 % Favored : 67.74 % 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: -2.47 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.016 0.002 PHE D 20 TYR 0.009 0.002 TYR D 10 ARG 0.004 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.355 Fit side-chains REVERT: A 3 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: A 5 ARG cc_start: 0.8372 (mtp180) cc_final: 0.6251 (pmt170) REVERT: B 3 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: B 5 ARG cc_start: 0.8491 (mtp180) cc_final: 0.6220 (pmt170) REVERT: B 28 LYS cc_start: 0.9124 (mttt) cc_final: 0.8642 (mttt) REVERT: C 3 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: C 5 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7950 (ttt-90) REVERT: C 22 GLU cc_start: 0.8670 (tt0) cc_final: 0.8461 (tt0) REVERT: C 23 ASP cc_start: 0.9143 (m-30) cc_final: 0.8824 (m-30) REVERT: C 28 LYS cc_start: 0.9301 (mttt) cc_final: 0.8918 (mttp) REVERT: D 3 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: D 5 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7632 (ttt180) REVERT: D 28 LYS cc_start: 0.9244 (mttt) cc_final: 0.8947 (mttm) REVERT: E 3 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: E 5 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7839 (tpt-90) REVERT: E 15 GLN cc_start: 0.9250 (tt0) cc_final: 0.9032 (tt0) REVERT: E 28 LYS cc_start: 0.9180 (mttt) cc_final: 0.8876 (mttp) REVERT: F 3 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: F 28 LYS cc_start: 0.9140 (mttt) cc_final: 0.8812 (mtpt) REVERT: G 3 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: G 5 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7661 (ttt-90) REVERT: G 7 ASP cc_start: 0.8550 (p0) cc_final: 0.8188 (p0) REVERT: G 28 LYS cc_start: 0.9296 (mttt) cc_final: 0.8949 (mttp) REVERT: H 3 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: H 5 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8002 (ttt-90) REVERT: H 28 LYS cc_start: 0.9260 (mttt) cc_final: 0.8931 (mttm) REVERT: I 3 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: I 5 ARG cc_start: 0.8066 (mtp180) cc_final: 0.6542 (tpm170) REVERT: I 28 LYS cc_start: 0.9216 (mttm) cc_final: 0.8921 (mttm) REVERT: J 3 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: J 5 ARG cc_start: 0.8088 (mtp180) cc_final: 0.6696 (tpm170) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 1.4635 time to fit residues: 183.6393 Evaluate side-chains 122 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.118621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091782 restraints weight = 3919.962| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.24 r_work: 0.3465 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3120 Z= 0.185 Angle : 0.475 7.876 4190 Z= 0.253 Chirality : 0.052 0.130 440 Planarity : 0.001 0.011 560 Dihedral : 10.252 59.775 450 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 7.42 % Allowed : 24.84 % Favored : 67.74 % 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: -2.70 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 6 PHE 0.007 0.001 PHE F 20 TYR 0.006 0.001 TYR E 10 ARG 0.003 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: A 5 ARG cc_start: 0.8386 (mtp180) cc_final: 0.6190 (pmt170) REVERT: B 3 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6631 (pm20) REVERT: B 28 LYS cc_start: 0.8840 (mttt) cc_final: 0.8369 (mttt) REVERT: C 3 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: C 22 GLU cc_start: 0.8463 (tt0) cc_final: 0.8166 (tt0) REVERT: C 28 LYS cc_start: 0.9274 (mttt) cc_final: 0.8902 (mttp) REVERT: D 3 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: D 5 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7638 (ttt180) REVERT: E 3 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: E 5 ARG cc_start: 0.8445 (ttp80) cc_final: 0.7879 (tpt-90) REVERT: E 28 LYS cc_start: 0.9048 (mttt) cc_final: 0.8707 (mttp) REVERT: F 3 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: F 28 LYS cc_start: 0.9031 (mttt) cc_final: 0.8682 (mtpt) REVERT: F 40 VAL cc_start: 0.8640 (m) cc_final: 0.8387 (p) REVERT: G 3 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: G 5 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7772 (ttt-90) REVERT: G 7 ASP cc_start: 0.8503 (p0) cc_final: 0.8063 (p0) REVERT: G 28 LYS cc_start: 0.9141 (mttt) cc_final: 0.8701 (mttp) REVERT: H 3 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: H 5 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8127 (ttt-90) REVERT: H 28 LYS cc_start: 0.9198 (mttt) cc_final: 0.8835 (mttm) REVERT: I 3 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: I 5 ARG cc_start: 0.7842 (mtp180) cc_final: 0.6648 (tpm170) REVERT: I 28 LYS cc_start: 0.9133 (mttm) cc_final: 0.8806 (mttm) REVERT: J 3 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: J 5 ARG cc_start: 0.7982 (mtp180) cc_final: 0.6665 (tpm170) outliers start: 23 outliers final: 6 residues processed: 108 average time/residue: 1.2458 time to fit residues: 137.6395 Evaluate side-chains 108 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.115125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086953 restraints weight = 3904.745| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.23 r_work: 0.3341 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 3120 Z= 0.426 Angle : 0.532 7.550 4190 Z= 0.284 Chirality : 0.052 0.126 440 Planarity : 0.002 0.011 560 Dihedral : 10.400 59.817 450 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 8.39 % Allowed : 23.55 % Favored : 68.06 % 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: -2.65 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 14 PHE 0.010 0.001 PHE D 20 TYR 0.013 0.002 TYR J 10 ARG 0.002 0.001 ARG H 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.344 Fit side-chains REVERT: A 3 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: A 5 ARG cc_start: 0.8466 (mtp180) cc_final: 0.6156 (pmt170) REVERT: B 3 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: B 28 LYS cc_start: 0.8959 (mttt) cc_final: 0.8703 (mttm) REVERT: C 3 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: C 5 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8003 (ttt-90) REVERT: C 22 GLU cc_start: 0.8584 (tt0) cc_final: 0.8378 (tt0) REVERT: C 28 LYS cc_start: 0.9264 (mttt) cc_final: 0.8907 (mttp) REVERT: C 32 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (mt) REVERT: D 3 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: D 5 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7814 (ttt180) REVERT: D 28 LYS cc_start: 0.9293 (mttt) cc_final: 0.8999 (mttm) REVERT: E 3 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: E 5 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7957 (tpt-90) REVERT: E 28 LYS cc_start: 0.9087 (mttt) cc_final: 0.8753 (mttp) REVERT: F 3 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: F 40 VAL cc_start: 0.8640 (m) cc_final: 0.8347 (p) REVERT: G 3 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: G 5 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7720 (ttt-90) REVERT: G 7 ASP cc_start: 0.8507 (p0) cc_final: 0.8158 (p0) REVERT: G 28 LYS cc_start: 0.9248 (mttt) cc_final: 0.8853 (mttp) REVERT: G 32 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8951 (mt) REVERT: H 3 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: H 5 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8131 (ttt-90) REVERT: H 28 LYS cc_start: 0.9259 (mttt) cc_final: 0.8927 (mttp) REVERT: I 3 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: I 5 ARG cc_start: 0.7863 (mtp180) cc_final: 0.6609 (tpm170) REVERT: I 28 LYS cc_start: 0.9147 (mttm) cc_final: 0.8829 (mttm) REVERT: J 3 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (mm-30) outliers start: 26 outliers final: 4 residues processed: 113 average time/residue: 1.2412 time to fit residues: 143.5206 Evaluate side-chains 111 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 64.8297 > 50: distance: 15 - 133: 11.286 distance: 18 - 151: 12.720 distance: 31 - 154: 8.190 distance: 128 - 130: 5.962 distance: 130 - 131: 10.724 distance: 131 - 132: 6.381 distance: 131 - 134: 7.177 distance: 132 - 133: 8.374 distance: 134 - 135: 7.924 distance: 135 - 136: 10.056 distance: 135 - 137: 10.209 distance: 136 - 138: 8.944 distance: 137 - 139: 21.262 distance: 138 - 140: 5.118 distance: 139 - 140: 16.963 distance: 140 - 141: 11.312 distance: 142 - 143: 8.771 distance: 143 - 144: 15.891 distance: 143 - 146: 12.018 distance: 144 - 145: 10.459 distance: 144 - 151: 23.086 distance: 146 - 147: 12.634 distance: 147 - 148: 7.173 distance: 148 - 149: 16.548 distance: 148 - 150: 11.950 distance: 151 - 152: 16.392 distance: 152 - 153: 10.381 distance: 152 - 155: 6.197 distance: 153 - 154: 8.998 distance: 153 - 158: 5.544 distance: 155 - 156: 13.125 distance: 155 - 157: 13.631 distance: 158 - 159: 4.967 distance: 159 - 160: 6.724 distance: 159 - 162: 9.819 distance: 160 - 161: 11.601 distance: 160 - 168: 5.905 distance: 162 - 163: 8.616 distance: 163 - 164: 11.198 distance: 163 - 165: 26.909 distance: 164 - 166: 5.338 distance: 165 - 167: 13.834 distance: 166 - 167: 3.948 distance: 168 - 169: 10.524 distance: 169 - 170: 7.695 distance: 169 - 172: 13.931 distance: 170 - 171: 8.298 distance: 170 - 178: 3.452 distance: 173 - 174: 5.350 distance: 173 - 175: 8.316 distance: 174 - 176: 7.917 distance: 175 - 177: 9.190 distance: 176 - 177: 8.231 distance: 178 - 179: 17.422 distance: 179 - 180: 18.625 distance: 179 - 182: 10.385 distance: 180 - 181: 9.442 distance: 180 - 187: 10.769 distance: 182 - 183: 20.142 distance: 183 - 184: 29.120 distance: 184 - 185: 18.054 distance: 184 - 186: 18.692 distance: 187 - 188: 16.227 distance: 188 - 189: 16.693 distance: 188 - 191: 6.823 distance: 189 - 190: 17.617 distance: 189 - 196: 21.260 distance: 191 - 192: 16.267 distance: 192 - 193: 6.604 distance: 193 - 194: 18.940 distance: 194 - 195: 23.762 distance: 196 - 197: 27.270 distance: 197 - 198: 32.878 distance: 197 - 200: 38.467 distance: 198 - 199: 8.860 distance: 198 - 204: 38.004 distance: 200 - 201: 21.894 distance: 201 - 202: 17.426 distance: 201 - 203: 38.824 distance: 204 - 205: 30.164 distance: 205 - 206: 13.195 distance: 205 - 208: 30.627 distance: 206 - 207: 13.441 distance: 206 - 211: 14.204 distance: 208 - 209: 7.479 distance: 208 - 210: 22.907 distance: 211 - 212: 10.909 distance: 212 - 215: 13.865 distance: 213 - 214: 6.353 distance: 213 - 222: 5.710 distance: 215 - 216: 9.962 distance: 216 - 217: 4.980 distance: 216 - 218: 5.824 distance: 217 - 219: 6.289 distance: 218 - 220: 9.344 distance: 219 - 221: 17.746 distance: 220 - 221: 10.778