Starting phenix.real_space_refine on Sat Aug 23 00:32:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cp9_30421/08_2025/7cp9_30421.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.051 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 36 5.16 5 C 5572 2.51 5 N 1390 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "F" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.30 Number of scatterers: 8530 At special positions: 0 Unit cell: (122.694, 140.946, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 11 15.00 O 1521 8.00 N 1390 7.00 C 5572 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 488.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 39.5% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 41 Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.419A pdb=" N LEU A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 40 removed outlier: 4.086A pdb=" N MET B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.912A pdb=" N LEU B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.630A pdb=" N ASP C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 60 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.631A pdb=" N ASP D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 60 Processing helix chain 'E' and resid 5 through 38 removed outlier: 5.665A pdb=" N ILE E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix removed outlier: 4.156A pdb=" N ARG E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'F' and resid 5 through 38 removed outlier: 5.664A pdb=" N ILE F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 4.156A pdb=" N ARG F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 58 through 96 removed outlier: 4.092A pdb=" N ALA G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 117 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 58 through 96 removed outlier: 4.091A pdb=" N ALA H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 117 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.603A pdb=" N ARG I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS I 90 " --> pdb=" O CYS I 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 92 removed outlier: 3.602A pdb=" N ARG J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS J 90 " --> pdb=" O CYS J 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 100 through 107 removed outlier: 6.203A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU I 337 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 107 removed outlier: 6.203A pdb=" N GLN J 181 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU J 337 " --> pdb=" O LEU J 332 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1620 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: 1.40 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1316 1.30 - 1.43: 2165 1.43 - 1.56: 5121 1.56 - 1.68: 23 1.68 - 1.81: 62 Bond restraints: 8687 Sorted by residual: bond pdb=" C31 PC1 E 102 " pdb=" O31 PC1 E 102 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 PC1 E 102 " pdb=" O21 PC1 E 102 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C21 PC1 C 101 " pdb=" O21 PC1 C 101 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C31 PC1 F 102 " pdb=" O31 PC1 F 102 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C31 PC1 G 202 " pdb=" O31 PC1 G 202 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 8682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 11070 2.94 - 5.87: 510 5.87 - 8.81: 31 8.81 - 11.75: 18 11.75 - 14.69: 11 Bond angle restraints: 11640 Sorted by residual: angle pdb=" O12 PC1 C 101 " pdb=" P PC1 C 101 " pdb=" O14 PC1 C 101 " ideal model delta sigma weight residual 123.67 108.98 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O12 PC1 E 102 " pdb=" P PC1 E 102 " pdb=" O14 PC1 E 102 " ideal model delta sigma weight residual 123.67 108.99 14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O12 PC1 G 201 " pdb=" P PC1 G 201 " pdb=" O14 PC1 G 201 " ideal model delta sigma weight residual 123.67 109.09 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O12 PC1 G 202 " pdb=" P PC1 G 202 " pdb=" O14 PC1 G 202 " ideal model delta sigma weight residual 123.67 109.22 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" O12 PC1 F 101 " pdb=" P PC1 F 101 " pdb=" O14 PC1 F 101 " ideal model delta sigma weight residual 123.67 109.23 14.44 3.00e+00 1.11e-01 2.32e+01 ... (remaining 11635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4649 17.61 - 35.21: 437 35.21 - 52.82: 182 52.82 - 70.42: 50 70.42 - 88.03: 21 Dihedral angle restraints: 5339 sinusoidal: 2434 harmonic: 2905 Sorted by residual: dihedral pdb=" CA LYS A 47 " pdb=" C LYS A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU A 45 " pdb=" C LEU A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 849 0.038 - 0.075: 289 0.075 - 0.113: 87 0.113 - 0.151: 15 0.151 - 0.189: 1 Chirality restraints: 1241 Sorted by residual: chirality pdb=" CA THR A 41 " pdb=" N THR A 41 " pdb=" C THR A 41 " pdb=" CB THR A 41 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ASP I 198 " pdb=" N ASP I 198 " pdb=" C ASP I 198 " pdb=" CB ASP I 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ASP J 198 " pdb=" N ASP J 198 " pdb=" C ASP J 198 " pdb=" CB ASP J 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1238 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 41 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO B 42 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 332 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO J 333 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 333 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 333 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 332 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 333 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 333 " -0.027 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 595 2.73 - 3.27: 7923 3.27 - 3.81: 12858 3.81 - 4.36: 14991 4.36 - 4.90: 27520 Nonbonded interactions: 63887 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" OE1 GLN J 223 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR I 221 " pdb=" OE1 GLN I 223 " model vdw 2.183 3.040 nonbonded pdb=" OG SER I 122 " pdb=" O ILE I 124 " model vdw 2.263 3.040 nonbonded pdb=" OG SER J 122 " pdb=" O ILE J 124 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG1 THR C 17 " model vdw 2.266 3.040 ... (remaining 63882 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 11 through 47) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 15 through 63) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 29 through 202) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 76 through 361) } 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.210 Find NCS groups from input model: 0.130 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.007 0.072 8688 Z= 0.371 Angle : 1.241 14.685 11640 Z= 0.522 Chirality : 0.042 0.189 1241 Planarity : 0.004 0.056 1431 Dihedral : 17.402 88.028 3469 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 7.05 % Allowed : 10.04 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.25), residues: 997 helix: -0.82 (0.25), residues: 368 sheet: -1.22 (0.25), residues: 380 loop : -3.24 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.009 0.001 TYR J 275 PHE 0.017 0.002 PHE A 43 TRP 0.010 0.001 TRP D 57 HIS 0.003 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 8687) covalent geometry : angle 1.24078 (11640) hydrogen bonds : bond 0.09341 ( 568) hydrogen bonds : angle 4.86580 ( 1620) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4913 (tpp-160) REVERT: C 57 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.5115 (m100) REVERT: D 57 TRP cc_start: 0.3468 (OUTLIER) cc_final: 0.2925 (t-100) REVERT: F 34 LEU cc_start: 0.9042 (mt) cc_final: 0.8704 (mt) REVERT: G 76 LYS cc_start: 0.7863 (mptm) cc_final: 0.7212 (mmpt) REVERT: G 78 TYR cc_start: 0.8715 (t80) cc_final: 0.8387 (t80) REVERT: H 78 TYR cc_start: 0.8841 (t80) cc_final: 0.8619 (t80) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8729 (m) REVERT: H 109 GLU cc_start: 0.7017 (tt0) cc_final: 0.6808 (tt0) REVERT: I 265 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8251 (mm) REVERT: I 297 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8667 (m) REVERT: J 306 ASP cc_start: 0.7594 (p0) cc_final: 0.7253 (p0) outliers start: 59 outliers final: 21 residues processed: 301 average time/residue: 0.5716 time to fit residues: 182.4577 Evaluate side-chains 229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 289 GLU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN I 163 GLN I 220 HIS I 295 GLN J 111 ASN J 163 GLN J 166 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148999 restraints weight = 12025.698| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.88 r_work: 0.3757 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8688 Z= 0.190 Angle : 0.715 7.999 11640 Z= 0.360 Chirality : 0.044 0.205 1241 Planarity : 0.005 0.041 1431 Dihedral : 17.124 96.119 1656 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.77 % Allowed : 21.27 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.26), residues: 997 helix: 0.32 (0.27), residues: 378 sheet: -1.05 (0.25), residues: 396 loop : -2.47 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.017 0.002 TYR I 275 PHE 0.023 0.002 PHE G 67 TRP 0.012 0.001 TRP I 188 HIS 0.005 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8687) covalent geometry : angle 0.71497 (11640) hydrogen bonds : bond 0.04346 ( 568) hydrogen bonds : angle 4.38977 ( 1620) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.6776 (mmmm) cc_final: 0.6333 (mmtp) REVERT: B 47 LYS cc_start: 0.8129 (tttp) cc_final: 0.6149 (ttpt) REVERT: C 38 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4628 (tpp-160) REVERT: D 57 TRP cc_start: 0.4044 (OUTLIER) cc_final: 0.2942 (t-100) REVERT: F 34 LEU cc_start: 0.9130 (mt) cc_final: 0.8774 (mt) REVERT: G 76 LYS cc_start: 0.8060 (mptm) cc_final: 0.7554 (mmpt) REVERT: G 77 MET cc_start: 0.8244 (ptt) cc_final: 0.7924 (ptp) REVERT: G 78 TYR cc_start: 0.8829 (t80) cc_final: 0.8574 (t80) REVERT: H 78 TYR cc_start: 0.8912 (t80) cc_final: 0.8679 (t80) REVERT: H 81 SER cc_start: 0.8967 (t) cc_final: 0.8758 (m) REVERT: H 109 GLU cc_start: 0.7524 (tt0) cc_final: 0.7285 (tt0) REVERT: H 117 ARG cc_start: 0.4050 (tmm160) cc_final: 0.1806 (mmm-85) REVERT: I 240 ARG cc_start: 0.7455 (mpp80) cc_final: 0.7190 (mpp80) REVERT: I 315 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8702 (mtmm) REVERT: J 84 GLU cc_start: 0.8206 (pm20) cc_final: 0.7925 (pp20) REVERT: J 114 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: J 176 MET cc_start: 0.7672 (mpt) cc_final: 0.7389 (mpt) outliers start: 65 outliers final: 32 residues processed: 249 average time/residue: 0.5445 time to fit residues: 144.1656 Evaluate side-chains 232 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN I 140 GLN I 220 HIS I 295 GLN J 111 ASN J 163 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150812 restraints weight = 11880.640| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.85 r_work: 0.3787 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8688 Z= 0.137 Angle : 0.667 12.489 11640 Z= 0.332 Chirality : 0.042 0.184 1241 Planarity : 0.004 0.043 1431 Dihedral : 16.503 88.289 1644 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 7.53 % Allowed : 23.18 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.27), residues: 997 helix: 0.85 (0.27), residues: 378 sheet: -0.79 (0.25), residues: 396 loop : -2.07 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 38 TYR 0.019 0.001 TYR B 34 PHE 0.024 0.001 PHE B 31 TRP 0.009 0.001 TRP I 188 HIS 0.004 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8687) covalent geometry : angle 0.66700 (11640) hydrogen bonds : bond 0.03880 ( 568) hydrogen bonds : angle 4.28063 ( 1620) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7400 (mmp80) REVERT: B 19 LYS cc_start: 0.6746 (mmmm) cc_final: 0.6317 (mmtp) REVERT: B 47 LYS cc_start: 0.8063 (tttp) cc_final: 0.6049 (ttpt) REVERT: C 38 ARG cc_start: 0.5165 (OUTLIER) cc_final: 0.4603 (tpp-160) REVERT: C 49 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7654 (mp) REVERT: D 49 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7533 (tt) REVERT: D 57 TRP cc_start: 0.4168 (OUTLIER) cc_final: 0.2868 (t-100) REVERT: F 34 LEU cc_start: 0.9128 (mt) cc_final: 0.8786 (mt) REVERT: G 76 LYS cc_start: 0.8031 (mptm) cc_final: 0.7462 (mmtt) REVERT: G 77 MET cc_start: 0.8191 (ptt) cc_final: 0.7891 (ptp) REVERT: G 78 TYR cc_start: 0.8867 (t80) cc_final: 0.8583 (t80) REVERT: G 106 LEU cc_start: 0.9014 (tp) cc_final: 0.8668 (tt) REVERT: H 54 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6332 (pmm) REVERT: H 78 TYR cc_start: 0.8894 (t80) cc_final: 0.8690 (t80) REVERT: H 81 SER cc_start: 0.8912 (t) cc_final: 0.8676 (m) REVERT: H 109 GLU cc_start: 0.7521 (tt0) cc_final: 0.7282 (tt0) REVERT: H 117 ARG cc_start: 0.3752 (OUTLIER) cc_final: 0.1394 (mmm-85) REVERT: I 315 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8707 (mtmm) REVERT: J 176 MET cc_start: 0.7668 (mpt) cc_final: 0.7393 (mpt) REVERT: J 180 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8822 (t) REVERT: J 280 ASP cc_start: 0.8628 (m-30) cc_final: 0.8421 (m-30) REVERT: J 294 MET cc_start: 0.8392 (mpm) cc_final: 0.8169 (mmp) REVERT: J 337 LEU cc_start: 0.8825 (tp) cc_final: 0.8583 (mt) outliers start: 63 outliers final: 33 residues processed: 240 average time/residue: 0.5276 time to fit residues: 135.2194 Evaluate side-chains 242 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.0170 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 GLN I 140 GLN I 220 HIS ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149505 restraints weight = 12099.534| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.87 r_work: 0.3767 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8688 Z= 0.169 Angle : 0.685 10.455 11640 Z= 0.339 Chirality : 0.043 0.186 1241 Planarity : 0.004 0.045 1431 Dihedral : 16.205 87.760 1642 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 9.20 % Allowed : 23.18 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.27), residues: 997 helix: 1.03 (0.27), residues: 376 sheet: -0.55 (0.25), residues: 396 loop : -1.95 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 60 TYR 0.021 0.002 TYR B 34 PHE 0.029 0.002 PHE G 67 TRP 0.010 0.001 TRP D 57 HIS 0.005 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8687) covalent geometry : angle 0.68477 (11640) hydrogen bonds : bond 0.04034 ( 568) hydrogen bonds : angle 4.30829 ( 1620) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 204 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7379 (mmm160) REVERT: B 47 LYS cc_start: 0.8137 (tttp) cc_final: 0.6025 (ttpt) REVERT: C 38 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.4834 (tpp-160) REVERT: C 43 ARG cc_start: 0.7832 (tmt-80) cc_final: 0.7076 (ptm160) REVERT: C 49 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7685 (mp) REVERT: D 57 TRP cc_start: 0.4237 (OUTLIER) cc_final: 0.2835 (t-100) REVERT: F 34 LEU cc_start: 0.9154 (mt) cc_final: 0.8804 (mt) REVERT: G 76 LYS cc_start: 0.8033 (mptm) cc_final: 0.7464 (mmtt) REVERT: G 77 MET cc_start: 0.8143 (ptt) cc_final: 0.7812 (ptp) REVERT: G 78 TYR cc_start: 0.8903 (t80) cc_final: 0.8619 (t80) REVERT: H 54 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6599 (pmm) REVERT: H 79 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7103 (tmt170) REVERT: H 81 SER cc_start: 0.8942 (t) cc_final: 0.8679 (m) REVERT: H 109 GLU cc_start: 0.7562 (tt0) cc_final: 0.7320 (tt0) REVERT: H 117 ARG cc_start: 0.4019 (OUTLIER) cc_final: 0.1673 (mmm-85) REVERT: I 315 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8673 (mtmm) REVERT: J 84 GLU cc_start: 0.7954 (pp20) cc_final: 0.6984 (pp20) REVERT: J 114 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: J 176 MET cc_start: 0.7663 (mpt) cc_final: 0.7414 (mpt) REVERT: J 180 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8816 (t) REVERT: J 337 LEU cc_start: 0.8839 (tp) cc_final: 0.8627 (mt) outliers start: 77 outliers final: 38 residues processed: 251 average time/residue: 0.5404 time to fit residues: 144.5836 Evaluate side-chains 248 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 30.0000 chunk 67 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149433 restraints weight = 11945.724| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.84 r_work: 0.3773 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8688 Z= 0.168 Angle : 0.696 10.867 11640 Z= 0.343 Chirality : 0.043 0.185 1241 Planarity : 0.004 0.045 1431 Dihedral : 15.943 89.765 1637 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 7.53 % Allowed : 26.28 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.27), residues: 997 helix: 1.09 (0.27), residues: 376 sheet: -0.33 (0.26), residues: 394 loop : -1.75 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.019 0.002 TYR J 275 PHE 0.025 0.001 PHE B 31 TRP 0.010 0.001 TRP D 57 HIS 0.005 0.001 HIS J 112 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8687) covalent geometry : angle 0.69633 (11640) hydrogen bonds : bond 0.03998 ( 568) hydrogen bonds : angle 4.28337 ( 1620) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6331 (t0) REVERT: B 19 LYS cc_start: 0.6835 (mmmm) cc_final: 0.6377 (mmtp) REVERT: B 47 LYS cc_start: 0.8075 (tttp) cc_final: 0.5995 (ttpt) REVERT: C 38 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4833 (tpp80) REVERT: C 43 ARG cc_start: 0.7985 (tmt-80) cc_final: 0.7696 (ptm-80) REVERT: D 57 TRP cc_start: 0.4183 (OUTLIER) cc_final: 0.2344 (t-100) REVERT: F 34 LEU cc_start: 0.9148 (mt) cc_final: 0.8790 (mt) REVERT: G 76 LYS cc_start: 0.7981 (mptm) cc_final: 0.7418 (mmtt) REVERT: G 77 MET cc_start: 0.8175 (ptt) cc_final: 0.7807 (ptp) REVERT: G 78 TYR cc_start: 0.8901 (t80) cc_final: 0.8671 (t80) REVERT: G 107 GLN cc_start: 0.8349 (tp40) cc_final: 0.7943 (tm-30) REVERT: H 54 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6420 (pmm) REVERT: H 79 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7131 (tmt170) REVERT: H 81 SER cc_start: 0.8919 (t) cc_final: 0.8645 (m) REVERT: H 109 GLU cc_start: 0.7575 (tt0) cc_final: 0.7356 (tt0) REVERT: H 117 ARG cc_start: 0.4131 (OUTLIER) cc_final: 0.1802 (mmm-85) REVERT: I 112 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8115 (m170) REVERT: I 294 MET cc_start: 0.8462 (mmm) cc_final: 0.8155 (mpp) REVERT: I 315 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: J 84 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: J 114 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: J 155 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7983 (t70) REVERT: J 180 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8789 (t) REVERT: J 240 ARG cc_start: 0.7255 (mpp80) cc_final: 0.6902 (mtm180) outliers start: 63 outliers final: 35 residues processed: 241 average time/residue: 0.5565 time to fit residues: 142.4219 Evaluate side-chains 246 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 315 LYS Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 4 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.174603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151079 restraints weight = 11903.753| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.85 r_work: 0.3789 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8688 Z= 0.137 Angle : 0.676 11.205 11640 Z= 0.332 Chirality : 0.042 0.190 1241 Planarity : 0.004 0.045 1431 Dihedral : 15.588 89.867 1636 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 7.53 % Allowed : 27.12 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.28), residues: 997 helix: 1.28 (0.27), residues: 376 sheet: -0.12 (0.26), residues: 394 loop : -1.71 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 60 TYR 0.019 0.002 TYR J 275 PHE 0.025 0.001 PHE B 31 TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8687) covalent geometry : angle 0.67556 (11640) hydrogen bonds : bond 0.03704 ( 568) hydrogen bonds : angle 4.19425 ( 1620) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6297 (t0) REVERT: B 47 LYS cc_start: 0.8060 (tttp) cc_final: 0.5941 (ttpt) REVERT: C 38 ARG cc_start: 0.5200 (OUTLIER) cc_final: 0.4617 (tpp80) REVERT: C 43 ARG cc_start: 0.7970 (tmt-80) cc_final: 0.7711 (ptm-80) REVERT: C 49 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7696 (mp) REVERT: D 57 TRP cc_start: 0.4120 (OUTLIER) cc_final: 0.2154 (t-100) REVERT: F 34 LEU cc_start: 0.9130 (mt) cc_final: 0.8793 (mt) REVERT: G 76 LYS cc_start: 0.8002 (mptm) cc_final: 0.7415 (mmtt) REVERT: G 77 MET cc_start: 0.8183 (ptt) cc_final: 0.7849 (ptp) REVERT: G 78 TYR cc_start: 0.8884 (t80) cc_final: 0.8642 (t80) REVERT: H 54 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6385 (pmm) REVERT: H 79 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7117 (tmt170) REVERT: H 81 SER cc_start: 0.8917 (t) cc_final: 0.8629 (m) REVERT: H 109 GLU cc_start: 0.7608 (tt0) cc_final: 0.7382 (tt0) REVERT: H 117 ARG cc_start: 0.4169 (OUTLIER) cc_final: 0.1836 (mmm-85) REVERT: I 112 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8128 (m170) REVERT: I 267 GLN cc_start: 0.7278 (tp40) cc_final: 0.6806 (tm-30) REVERT: I 294 MET cc_start: 0.8471 (mmm) cc_final: 0.8098 (mpp) REVERT: J 84 GLU cc_start: 0.7828 (pp20) cc_final: 0.6851 (pp20) REVERT: J 114 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: J 180 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8779 (t) outliers start: 63 outliers final: 35 residues processed: 241 average time/residue: 0.5579 time to fit residues: 142.9235 Evaluate side-chains 239 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 181 GLN Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN H 110 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS I 295 GLN J 181 GLN J 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150609 restraints weight = 12084.326| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.85 r_work: 0.3781 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8688 Z= 0.150 Angle : 0.691 11.126 11640 Z= 0.337 Chirality : 0.042 0.182 1241 Planarity : 0.004 0.046 1431 Dihedral : 15.480 89.514 1635 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.05 % Allowed : 28.08 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.28), residues: 997 helix: 1.35 (0.27), residues: 376 sheet: -0.04 (0.26), residues: 394 loop : -1.73 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 60 TYR 0.023 0.001 TYR B 34 PHE 0.029 0.001 PHE B 31 TRP 0.009 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8687) covalent geometry : angle 0.69066 (11640) hydrogen bonds : bond 0.03764 ( 568) hydrogen bonds : angle 4.20183 ( 1620) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6335 (t0) REVERT: B 47 LYS cc_start: 0.8076 (tttp) cc_final: 0.5957 (ttpt) REVERT: C 38 ARG cc_start: 0.5248 (OUTLIER) cc_final: 0.4646 (tpp80) REVERT: C 43 ARG cc_start: 0.7916 (tmt-80) cc_final: 0.7680 (ptm-80) REVERT: C 49 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7677 (mp) REVERT: D 57 TRP cc_start: 0.4229 (OUTLIER) cc_final: 0.3717 (m100) REVERT: F 34 LEU cc_start: 0.9148 (mt) cc_final: 0.8800 (mt) REVERT: G 76 LYS cc_start: 0.8016 (mptm) cc_final: 0.7405 (mmtt) REVERT: G 77 MET cc_start: 0.8260 (ptt) cc_final: 0.7871 (ptp) REVERT: G 78 TYR cc_start: 0.8871 (t80) cc_final: 0.8635 (t80) REVERT: G 107 GLN cc_start: 0.8330 (tp40) cc_final: 0.7885 (tm-30) REVERT: H 54 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6293 (pmm) REVERT: H 77 MET cc_start: 0.6983 (ptt) cc_final: 0.5967 (ttp) REVERT: H 79 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7065 (tmt170) REVERT: H 81 SER cc_start: 0.8915 (t) cc_final: 0.8608 (m) REVERT: H 109 GLU cc_start: 0.7605 (tt0) cc_final: 0.7368 (tt0) REVERT: H 117 ARG cc_start: 0.4123 (OUTLIER) cc_final: 0.1788 (mmm-85) REVERT: I 112 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.8181 (m170) REVERT: J 114 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: J 180 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8823 (t) outliers start: 59 outliers final: 34 residues processed: 229 average time/residue: 0.5699 time to fit residues: 138.8835 Evaluate side-chains 239 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 HIS J 181 GLN J 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.175673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151986 restraints weight = 11910.610| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.85 r_work: 0.3798 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8688 Z= 0.130 Angle : 0.685 11.204 11640 Z= 0.334 Chirality : 0.042 0.231 1241 Planarity : 0.004 0.046 1431 Dihedral : 15.161 89.542 1635 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.21 % Allowed : 29.63 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.28), residues: 997 helix: 1.48 (0.27), residues: 378 sheet: 0.32 (0.27), residues: 378 loop : -1.73 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 60 TYR 0.020 0.001 TYR J 275 PHE 0.024 0.001 PHE B 31 TRP 0.010 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8687) covalent geometry : angle 0.68509 (11640) hydrogen bonds : bond 0.03528 ( 568) hydrogen bonds : angle 4.11949 ( 1620) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6390 (t0) REVERT: B 47 LYS cc_start: 0.8031 (tttp) cc_final: 0.5980 (ttpt) REVERT: C 38 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4561 (tpp80) REVERT: C 43 ARG cc_start: 0.7922 (tmt-80) cc_final: 0.7443 (ptm-80) REVERT: C 49 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7710 (mp) REVERT: D 57 TRP cc_start: 0.4262 (OUTLIER) cc_final: 0.3334 (m100) REVERT: F 34 LEU cc_start: 0.9124 (mt) cc_final: 0.8797 (mt) REVERT: G 76 LYS cc_start: 0.8047 (mptm) cc_final: 0.7326 (mmpt) REVERT: G 77 MET cc_start: 0.8255 (ptt) cc_final: 0.7903 (ptp) REVERT: G 78 TYR cc_start: 0.8870 (t80) cc_final: 0.8622 (t80) REVERT: G 107 GLN cc_start: 0.8333 (tp40) cc_final: 0.7939 (tm-30) REVERT: H 54 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6315 (pmm) REVERT: H 77 MET cc_start: 0.6921 (ptt) cc_final: 0.6079 (tpp) REVERT: H 79 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7157 (tmt170) REVERT: H 81 SER cc_start: 0.8885 (t) cc_final: 0.8573 (m) REVERT: H 117 ARG cc_start: 0.4041 (OUTLIER) cc_final: 0.1751 (mmm-85) REVERT: I 267 GLN cc_start: 0.7353 (tp40) cc_final: 0.6807 (tm-30) REVERT: I 294 MET cc_start: 0.8443 (mmm) cc_final: 0.8121 (mpp) REVERT: J 84 GLU cc_start: 0.7708 (pp20) cc_final: 0.6713 (pp20) REVERT: J 180 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (t) REVERT: J 348 ARG cc_start: 0.8258 (tpt90) cc_final: 0.7775 (tpp80) outliers start: 52 outliers final: 30 residues processed: 225 average time/residue: 0.5348 time to fit residues: 128.4623 Evaluate side-chains 229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 111 ASN Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.0370 chunk 92 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN H 110 GLN ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 HIS I 220 HIS ** I 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN J 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.174649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151348 restraints weight = 11929.999| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.82 r_work: 0.3793 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8688 Z= 0.142 Angle : 0.704 10.944 11640 Z= 0.341 Chirality : 0.042 0.180 1241 Planarity : 0.004 0.047 1431 Dihedral : 14.956 88.736 1630 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.62 % Allowed : 30.23 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.28), residues: 997 helix: 1.52 (0.27), residues: 376 sheet: 0.45 (0.27), residues: 374 loop : -1.69 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 60 TYR 0.022 0.001 TYR J 275 PHE 0.026 0.001 PHE B 31 TRP 0.011 0.001 TRP C 57 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8687) covalent geometry : angle 0.70372 (11640) hydrogen bonds : bond 0.03583 ( 568) hydrogen bonds : angle 4.14075 ( 1620) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.7955 (tmt-80) cc_final: 0.7480 (ptm-80) REVERT: C 49 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7722 (mp) REVERT: F 34 LEU cc_start: 0.9132 (mt) cc_final: 0.8799 (mt) REVERT: G 76 LYS cc_start: 0.7972 (mptm) cc_final: 0.7257 (mmpt) REVERT: G 77 MET cc_start: 0.8238 (ptt) cc_final: 0.7891 (ptp) REVERT: G 78 TYR cc_start: 0.8874 (t80) cc_final: 0.8632 (t80) REVERT: G 107 GLN cc_start: 0.8282 (tp40) cc_final: 0.7928 (tm-30) REVERT: H 54 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6353 (pmm) REVERT: H 77 MET cc_start: 0.6947 (ptt) cc_final: 0.6065 (tpp) REVERT: H 79 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7145 (tmt170) REVERT: H 81 SER cc_start: 0.8886 (t) cc_final: 0.8554 (m) REVERT: H 117 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.1806 (mmm-85) REVERT: I 112 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.8171 (m170) REVERT: I 267 GLN cc_start: 0.7276 (tp40) cc_final: 0.6727 (tm-30) REVERT: J 84 GLU cc_start: 0.7710 (pp20) cc_final: 0.6679 (pp20) REVERT: J 114 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: J 180 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8778 (t) REVERT: J 348 ARG cc_start: 0.8270 (tpt90) cc_final: 0.7798 (tpp80) outliers start: 47 outliers final: 27 residues processed: 221 average time/residue: 0.5150 time to fit residues: 121.3436 Evaluate side-chains 229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN H 110 GLN I 220 HIS J 163 GLN J 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.175494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151634 restraints weight = 11924.066| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.83 r_work: 0.3796 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8688 Z= 0.144 Angle : 0.703 10.893 11640 Z= 0.344 Chirality : 0.042 0.195 1241 Planarity : 0.004 0.047 1431 Dihedral : 14.769 87.522 1624 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.66 % Allowed : 31.18 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.28), residues: 997 helix: 1.53 (0.27), residues: 376 sheet: 0.20 (0.27), residues: 394 loop : -1.56 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 60 TYR 0.022 0.001 TYR J 275 PHE 0.025 0.001 PHE B 31 TRP 0.011 0.001 TRP D 57 HIS 0.004 0.001 HIS J 271 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8687) covalent geometry : angle 0.70306 (11640) hydrogen bonds : bond 0.03568 ( 568) hydrogen bonds : angle 4.13066 ( 1620) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.8014 (tmt-80) cc_final: 0.7547 (ptm-80) REVERT: C 49 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7716 (mp) REVERT: F 34 LEU cc_start: 0.9116 (mt) cc_final: 0.8789 (mt) REVERT: G 76 LYS cc_start: 0.7964 (mptm) cc_final: 0.7273 (mmpt) REVERT: G 77 MET cc_start: 0.8271 (ptt) cc_final: 0.7925 (ptp) REVERT: G 78 TYR cc_start: 0.8890 (t80) cc_final: 0.8658 (t80) REVERT: G 107 GLN cc_start: 0.8317 (tp40) cc_final: 0.8043 (tm-30) REVERT: H 54 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6397 (pmm) REVERT: H 77 MET cc_start: 0.6962 (ptt) cc_final: 0.6083 (tpp) REVERT: H 79 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7172 (tmt170) REVERT: H 81 SER cc_start: 0.8873 (t) cc_final: 0.8539 (m) REVERT: H 117 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.1801 (mmm-85) REVERT: I 112 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8173 (m170) REVERT: I 267 GLN cc_start: 0.7287 (tp40) cc_final: 0.6743 (tm-30) REVERT: I 294 MET cc_start: 0.8359 (mmm) cc_final: 0.8014 (mpp) REVERT: J 84 GLU cc_start: 0.7698 (pp20) cc_final: 0.6700 (pp20) REVERT: J 114 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: J 180 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8775 (t) REVERT: J 348 ARG cc_start: 0.8270 (tpt90) cc_final: 0.7836 (tpp80) outliers start: 39 outliers final: 29 residues processed: 220 average time/residue: 0.3922 time to fit residues: 92.3888 Evaluate side-chains 231 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 54 MET Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 112 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain J residue 114 GLN Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 235 LEU Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 287 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain J residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5141 > 50: distance: 11 - 18: 14.447 distance: 18 - 19: 24.554 distance: 19 - 20: 28.554 distance: 19 - 22: 38.718 distance: 20 - 21: 27.523 distance: 20 - 27: 24.843 distance: 21 - 54: 8.681 distance: 23 - 24: 3.716 distance: 24 - 25: 12.983 distance: 24 - 26: 6.787 distance: 27 - 28: 15.343 distance: 28 - 29: 4.704 distance: 28 - 31: 17.811 distance: 29 - 30: 36.733 distance: 29 - 33: 36.595 distance: 31 - 32: 3.266 distance: 33 - 34: 10.098 distance: 34 - 35: 4.093 distance: 34 - 37: 26.380 distance: 35 - 36: 5.529 distance: 35 - 43: 15.085 distance: 36 - 69: 42.443 distance: 37 - 38: 26.199 distance: 38 - 39: 35.577 distance: 38 - 40: 18.824 distance: 39 - 41: 9.854 distance: 40 - 42: 12.559 distance: 41 - 42: 9.618 distance: 43 - 44: 15.669 distance: 44 - 45: 6.373 distance: 44 - 47: 19.916 distance: 45 - 46: 16.379 distance: 45 - 54: 14.950 distance: 47 - 48: 41.153 distance: 48 - 49: 31.193 distance: 49 - 50: 16.745 distance: 50 - 51: 6.786 distance: 51 - 52: 9.834 distance: 51 - 53: 4.290 distance: 54 - 55: 29.203 distance: 55 - 56: 30.213 distance: 55 - 58: 38.475 distance: 56 - 57: 16.221 distance: 56 - 63: 43.564 distance: 58 - 59: 31.065 distance: 59 - 60: 10.851 distance: 60 - 61: 10.926 distance: 61 - 62: 16.854 distance: 63 - 64: 37.124 distance: 64 - 65: 32.652 distance: 64 - 67: 32.661 distance: 65 - 66: 11.713 distance: 65 - 69: 17.770 distance: 67 - 68: 27.203 distance: 70 - 71: 6.262 distance: 70 - 73: 30.235 distance: 71 - 72: 37.811 distance: 71 - 78: 13.844 distance: 73 - 74: 11.673 distance: 75 - 76: 10.114 distance: 79 - 82: 11.672 distance: 80 - 87: 47.331 distance: 82 - 83: 4.670 distance: 83 - 84: 27.483 distance: 84 - 85: 14.734 distance: 84 - 86: 13.350 distance: 87 - 88: 18.925 distance: 88 - 89: 10.727 distance: 88 - 91: 49.688 distance: 89 - 90: 19.634 distance: 89 - 95: 28.452 distance: 91 - 92: 15.637 distance: 92 - 93: 25.513 distance: 92 - 94: 31.714 distance: 95 - 96: 36.854 distance: 96 - 97: 9.052 distance: 96 - 99: 44.946 distance: 97 - 98: 40.557 distance: 97 - 106: 24.744 distance: 99 - 100: 30.044 distance: 100 - 101: 19.496 distance: 100 - 102: 33.743 distance: 101 - 103: 11.238 distance: 102 - 104: 5.632 distance: 103 - 105: 28.974 distance: 104 - 105: 10.491 distance: 122 - 141: 3.670 distance: 129 - 134: 3.037 distance: 149 - 175: 3.368