Starting phenix.real_space_refine on Mon Apr 28 05:00:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.map" model { file = "/net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chu_45602/04_2025/9chu_45602.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4555 2.51 5 N 1151 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7009 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3326 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 418} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2806 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.76 Number of scatterers: 7009 At special positions: 0 Unit cell: (64.6, 84.15, 152.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1255 8.00 N 1151 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 52.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 removed outlier: 3.891A pdb=" N PHE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 102 through 137 removed outlier: 3.543A pdb=" N CYS A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix removed outlier: 3.522A pdb=" N MET A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.581A pdb=" N VAL A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.736A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.561A pdb=" N ILE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.797A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 395 through 421 Proline residue: A 411 - end of helix removed outlier: 4.711A pdb=" N ILE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.536A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 4.183A pdb=" N LEU A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.829A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 4.194A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.713A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.719A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 347 through 368 Proline residue: B 354 - end of helix Processing helix chain 'C' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.142A pdb=" N LEU B 195 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.591A pdb=" N LEU B 113 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR B 112 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 324 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.607A pdb=" N THR C 21 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 106 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.549A pdb=" N LYS C 35 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 37 " --> pdb=" O GLY C 28 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 942 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: 1.83 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1848 1.33 - 1.45: 1331 1.45 - 1.57: 3925 1.57 - 1.69: 1 1.69 - 1.81: 73 Bond restraints: 7178 Sorted by residual: bond pdb=" C9 FK5 C 201 " pdb=" O4 FK5 C 201 " ideal model delta sigma weight residual 1.206 1.407 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C1 FK5 C 201 " pdb=" O2 FK5 C 201 " ideal model delta sigma weight residual 1.211 1.410 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C22 FK5 C 201 " pdb=" O9 FK5 C 201 " ideal model delta sigma weight residual 1.215 1.408 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C8 FK5 C 201 " pdb=" O3 FK5 C 201 " ideal model delta sigma weight residual 1.232 1.408 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C8 FK5 C 201 " pdb=" C9 FK5 C 201 " ideal model delta sigma weight residual 1.537 1.395 0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9446 2.32 - 4.64: 233 4.64 - 6.95: 46 6.95 - 9.27: 15 9.27 - 11.59: 3 Bond angle restraints: 9743 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" C VAL A 206 " ideal model delta sigma weight residual 113.20 101.61 11.59 9.60e-01 1.09e+00 1.46e+02 angle pdb=" N VAL A 420 " pdb=" CA VAL A 420 " pdb=" C VAL A 420 " ideal model delta sigma weight residual 110.30 103.53 6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N ASP A 423 " pdb=" CA ASP A 423 " pdb=" C ASP A 423 " ideal model delta sigma weight residual 111.33 103.40 7.93 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 110.20 119.73 -9.53 1.49e+00 4.50e-01 4.09e+01 angle pdb=" N GLN A 422 " pdb=" CA GLN A 422 " pdb=" C GLN A 422 " ideal model delta sigma weight residual 113.15 105.90 7.25 1.19e+00 7.06e-01 3.71e+01 ... (remaining 9738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4221 35.78 - 71.56: 80 71.56 - 107.34: 8 107.34 - 143.13: 0 143.13 - 178.91: 4 Dihedral angle restraints: 4313 sinusoidal: 1734 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual -86.00 -174.25 88.25 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta harmonic sigma weight residual 122.80 137.79 -14.99 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" C ARG A 175 " pdb=" N ARG A 175 " pdb=" CA ARG A 175 " pdb=" CB ARG A 175 " ideal model delta harmonic sigma weight residual -122.60 -136.04 13.44 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 4310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1075 0.132 - 0.264: 22 0.264 - 0.396: 3 0.396 - 0.529: 2 0.529 - 0.661: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA SER A 203 " pdb=" N SER A 203 " pdb=" C SER A 203 " pdb=" CB SER A 203 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ARG A 175 " pdb=" N ARG A 175 " pdb=" C ARG A 175 " pdb=" CB ARG A 175 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CAL E5E A 501 " pdb=" CAH E5E A 501 " pdb=" CAK E5E A 501 " pdb=" OAD E5E A 501 " both_signs ideal model delta sigma weight residual False -2.31 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1100 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 C 201 " 0.111 2.00e-02 2.50e+03 1.22e-01 1.87e+02 pdb=" C27 FK5 C 201 " -0.039 2.00e-02 2.50e+03 pdb=" C28 FK5 C 201 " -0.193 2.00e-02 2.50e+03 pdb=" C29 FK5 C 201 " 0.151 2.00e-02 2.50e+03 pdb=" C42 FK5 C 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 C 201 " -0.052 2.00e-02 2.50e+03 5.92e-02 4.38e+01 pdb=" C19 FK5 C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C20 FK5 C 201 " 0.095 2.00e-02 2.50e+03 pdb=" C21 FK5 C 201 " -0.072 2.00e-02 2.50e+03 pdb=" C37 FK5 C 201 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 430 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C VAL A 430 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 430 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR A 431 " -0.022 2.00e-02 2.50e+03 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 282 2.71 - 3.26: 7155 3.26 - 3.81: 10761 3.81 - 4.35: 12971 4.35 - 4.90: 22172 Nonbonded interactions: 53341 Sorted by model distance: nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" O LEU A 395 " model vdw 2.212 3.040 nonbonded pdb=" O GLY B 105 " pdb=" OH TYR B 112 " model vdw 2.221 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.260 3.040 nonbonded pdb=" O PHE B 238 " pdb=" NH1 ARG B 291 " model vdw 2.279 3.120 ... (remaining 53336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.210 Find NCS groups from input model: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.201 7180 Z= 0.415 Angle : 0.893 11.588 9747 Z= 0.519 Chirality : 0.060 0.661 1103 Planarity : 0.006 0.122 1231 Dihedral : 16.113 178.907 2643 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.41 % Allowed : 1.22 % Favored : 98.37 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.29), residues: 877 helix: 0.22 (0.25), residues: 435 sheet: -2.37 (0.60), residues: 66 loop : -1.43 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 59 HIS 0.014 0.001 HIS B 280 PHE 0.025 0.002 PHE A 223 TYR 0.018 0.002 TYR A 449 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.14401 ( 324) hydrogen bonds : angle 5.87809 ( 942) SS BOND : bond 0.00204 ( 2) SS BOND : angle 2.56779 ( 4) covalent geometry : bond 0.00834 ( 7178) covalent geometry : angle 0.89204 ( 9743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 193 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 315 ASN cc_start: 0.8603 (t0) cc_final: 0.8339 (t0) REVERT: C 11 ASP cc_start: 0.8247 (t70) cc_final: 0.7864 (t70) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.1867 time to fit residues: 31.3841 Evaluate side-chains 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147403 restraints weight = 8461.697| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.63 r_work: 0.3615 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7180 Z= 0.141 Angle : 0.599 6.098 9747 Z= 0.310 Chirality : 0.042 0.171 1103 Planarity : 0.004 0.032 1231 Dihedral : 13.778 176.083 1064 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 8.42 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 877 helix: 0.67 (0.26), residues: 439 sheet: -2.32 (0.56), residues: 75 loop : -1.30 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 59 HIS 0.005 0.001 HIS B 280 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR B 261 ARG 0.003 0.000 ARG B 291 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 324) hydrogen bonds : angle 4.45126 ( 942) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.83044 ( 4) covalent geometry : bond 0.00326 ( 7178) covalent geometry : angle 0.59885 ( 9743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 2.057 Fit side-chains REVERT: A 72 ILE cc_start: 0.8351 (mm) cc_final: 0.8102 (mm) REVERT: A 193 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7456 (t80) REVERT: A 259 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7268 (mpp) REVERT: B 315 ASN cc_start: 0.8846 (t0) cc_final: 0.8598 (t0) REVERT: C 5 GLU cc_start: 0.7402 (pm20) cc_final: 0.7165 (pm20) REVERT: C 11 ASP cc_start: 0.8224 (t70) cc_final: 0.7768 (t70) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.2451 time to fit residues: 42.5495 Evaluate side-chains 106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 269 GLN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141921 restraints weight = 8795.989| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.94 r_work: 0.3458 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7180 Z= 0.145 Angle : 0.583 7.930 9747 Z= 0.300 Chirality : 0.041 0.132 1103 Planarity : 0.003 0.029 1231 Dihedral : 13.481 175.128 1064 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.58 % Allowed : 12.23 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 877 helix: 0.81 (0.26), residues: 441 sheet: -2.29 (0.56), residues: 75 loop : -1.22 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 173 HIS 0.002 0.001 HIS B 280 PHE 0.014 0.001 PHE B 333 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 324) hydrogen bonds : angle 4.18502 ( 942) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.50156 ( 4) covalent geometry : bond 0.00344 ( 7178) covalent geometry : angle 0.58344 ( 9743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.342 Fit side-chains REVERT: A 72 ILE cc_start: 0.8231 (mm) cc_final: 0.8002 (mm) REVERT: A 99 TRP cc_start: 0.6827 (OUTLIER) cc_final: 0.5685 (t60) REVERT: A 193 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7536 (t80) REVERT: A 379 LYS cc_start: 0.8359 (pptt) cc_final: 0.8095 (pptt) REVERT: B 98 MET cc_start: 0.7931 (mmm) cc_final: 0.7670 (mmm) REVERT: B 102 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: B 298 PHE cc_start: 0.7490 (m-80) cc_final: 0.6885 (t80) REVERT: B 315 ASN cc_start: 0.8818 (t0) cc_final: 0.8603 (t0) REVERT: C 5 GLU cc_start: 0.7421 (pm20) cc_final: 0.7163 (pm20) REVERT: C 11 ASP cc_start: 0.8227 (t70) cc_final: 0.7755 (t70) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.2064 time to fit residues: 31.9687 Evaluate side-chains 106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143271 restraints weight = 8754.653| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.95 r_work: 0.3531 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7180 Z= 0.119 Angle : 0.549 13.228 9747 Z= 0.280 Chirality : 0.040 0.129 1103 Planarity : 0.003 0.029 1231 Dihedral : 13.198 174.857 1064 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.26 % Allowed : 13.32 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.30), residues: 877 helix: 1.06 (0.26), residues: 439 sheet: -2.19 (0.56), residues: 75 loop : -1.11 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.010 0.001 PHE A 242 TYR 0.010 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 324) hydrogen bonds : angle 3.96781 ( 942) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.43926 ( 4) covalent geometry : bond 0.00271 ( 7178) covalent geometry : angle 0.54893 ( 9743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.821 Fit side-chains REVERT: A 72 ILE cc_start: 0.8269 (mm) cc_final: 0.8007 (mm) REVERT: A 193 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 435 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 98 MET cc_start: 0.7591 (mmm) cc_final: 0.7285 (mmm) REVERT: B 102 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: C 11 ASP cc_start: 0.8208 (t70) cc_final: 0.7830 (t70) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1455 time to fit residues: 25.6268 Evaluate side-chains 113 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141948 restraints weight = 8709.955| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.87 r_work: 0.3483 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7180 Z= 0.153 Angle : 0.604 13.820 9747 Z= 0.303 Chirality : 0.041 0.128 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.243 175.293 1064 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.40 % Allowed : 15.22 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.30), residues: 877 helix: 0.99 (0.26), residues: 439 sheet: -2.14 (0.56), residues: 75 loop : -1.16 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.016 0.001 PHE B 333 TYR 0.017 0.001 TYR B 287 ARG 0.002 0.000 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 324) hydrogen bonds : angle 3.98517 ( 942) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.42939 ( 4) covalent geometry : bond 0.00370 ( 7178) covalent geometry : angle 0.60392 ( 9743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.784 Fit side-chains REVERT: A 72 ILE cc_start: 0.8239 (mm) cc_final: 0.7986 (mm) REVERT: A 193 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7702 (t80) REVERT: A 435 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7607 (t0) REVERT: B 50 MET cc_start: 0.7834 (ttm) cc_final: 0.7529 (mmm) REVERT: B 102 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 151 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: B 298 PHE cc_start: 0.7371 (m-80) cc_final: 0.6858 (t80) REVERT: C 5 GLU cc_start: 0.7336 (pm20) cc_final: 0.6944 (pm20) REVERT: C 11 ASP cc_start: 0.8236 (t70) cc_final: 0.7782 (t70) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 0.1547 time to fit residues: 25.7420 Evaluate side-chains 115 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145019 restraints weight = 8650.799| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.76 r_work: 0.3573 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7180 Z= 0.120 Angle : 0.558 13.847 9747 Z= 0.282 Chirality : 0.040 0.126 1103 Planarity : 0.003 0.030 1231 Dihedral : 13.150 175.345 1064 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.58 % Allowed : 16.30 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.30), residues: 877 helix: 1.11 (0.26), residues: 437 sheet: -2.02 (0.57), residues: 75 loop : -1.14 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 173 HIS 0.002 0.000 HIS B 280 PHE 0.012 0.001 PHE B 333 TYR 0.014 0.001 TYR B 287 ARG 0.003 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 324) hydrogen bonds : angle 3.90038 ( 942) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.38620 ( 4) covalent geometry : bond 0.00275 ( 7178) covalent geometry : angle 0.55799 ( 9743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.772 Fit side-chains REVERT: A 72 ILE cc_start: 0.8304 (mm) cc_final: 0.8036 (mm) REVERT: A 193 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7634 (t80) REVERT: A 435 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7629 (t0) REVERT: B 50 MET cc_start: 0.7709 (ttm) cc_final: 0.7460 (mmm) REVERT: B 70 ILE cc_start: 0.8094 (tp) cc_final: 0.7805 (tt) REVERT: B 102 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: B 151 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: B 298 PHE cc_start: 0.7295 (m-80) cc_final: 0.6851 (t80) REVERT: C 5 GLU cc_start: 0.7306 (pm20) cc_final: 0.6602 (pm20) REVERT: C 11 ASP cc_start: 0.8218 (t70) cc_final: 0.7790 (t70) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.1560 time to fit residues: 25.1886 Evaluate side-chains 114 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.169797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142925 restraints weight = 8669.174| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.82 r_work: 0.3402 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7180 Z= 0.157 Angle : 0.607 13.799 9747 Z= 0.303 Chirality : 0.041 0.125 1103 Planarity : 0.003 0.029 1231 Dihedral : 13.219 175.665 1064 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.26 % Allowed : 16.44 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.30), residues: 877 helix: 1.00 (0.26), residues: 440 sheet: -1.91 (0.58), residues: 75 loop : -1.16 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 173 HIS 0.002 0.001 HIS B 26 PHE 0.019 0.001 PHE B 333 TYR 0.012 0.001 TYR B 174 ARG 0.003 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 324) hydrogen bonds : angle 3.93598 ( 942) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.40645 ( 4) covalent geometry : bond 0.00382 ( 7178) covalent geometry : angle 0.60691 ( 9743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.718 Fit side-chains REVERT: A 72 ILE cc_start: 0.8271 (mm) cc_final: 0.7998 (mm) REVERT: A 193 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 259 MET cc_start: 0.7664 (tmm) cc_final: 0.7258 (mmt) REVERT: A 435 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7655 (t0) REVERT: B 70 ILE cc_start: 0.8124 (tp) cc_final: 0.7805 (tt) REVERT: B 98 MET cc_start: 0.7790 (mmm) cc_final: 0.7332 (mmm) REVERT: B 102 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: B 151 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: B 298 PHE cc_start: 0.7380 (m-80) cc_final: 0.6890 (t80) REVERT: B 328 MET cc_start: 0.7564 (ttp) cc_final: 0.7320 (ttp) REVERT: C 11 ASP cc_start: 0.8278 (t70) cc_final: 0.7820 (t70) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.1504 time to fit residues: 25.2417 Evaluate side-chains 123 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0558 > 50: distance: 43 - 60: 33.871 distance: 47 - 66: 32.541 distance: 52 - 70: 31.484 distance: 55 - 60: 33.588 distance: 56 - 78: 32.256 distance: 60 - 61: 34.263 distance: 61 - 62: 5.787 distance: 61 - 64: 6.932 distance: 62 - 63: 66.035 distance: 63 - 85: 40.478 distance: 64 - 65: 57.026 distance: 66 - 67: 60.526 distance: 67 - 68: 50.076 distance: 68 - 69: 20.611 distance: 68 - 70: 6.304 distance: 69 - 91: 59.324 distance: 70 - 71: 31.766 distance: 71 - 72: 15.407 distance: 71 - 74: 45.984 distance: 72 - 73: 32.421 distance: 72 - 78: 44.066 distance: 73 - 102: 34.574 distance: 74 - 75: 26.470 distance: 75 - 76: 65.222 distance: 75 - 77: 59.012 distance: 78 - 79: 18.873 distance: 79 - 80: 12.744 distance: 79 - 82: 42.900 distance: 80 - 81: 27.653 distance: 80 - 85: 50.524 distance: 82 - 83: 18.026 distance: 82 - 84: 39.185 distance: 85 - 86: 56.389 distance: 86 - 87: 39.565 distance: 86 - 89: 55.297 distance: 87 - 88: 40.898 distance: 89 - 90: 33.425 distance: 91 - 92: 7.620 distance: 92 - 93: 28.068 distance: 92 - 95: 18.615 distance: 93 - 94: 10.860 distance: 93 - 102: 42.059 distance: 95 - 96: 44.147 distance: 96 - 97: 32.415 distance: 96 - 98: 49.353 distance: 97 - 99: 37.338 distance: 98 - 100: 51.429 distance: 99 - 101: 14.046 distance: 100 - 101: 20.888 distance: 102 - 103: 39.000 distance: 103 - 104: 57.955 distance: 103 - 106: 12.635 distance: 104 - 105: 26.065 distance: 104 - 110: 42.968 distance: 106 - 107: 17.331 distance: 107 - 108: 14.915 distance: 107 - 109: 29.140 distance: 110 - 111: 38.107 distance: 110 - 116: 17.902 distance: 111 - 112: 41.910 distance: 111 - 114: 7.230 distance: 112 - 113: 12.612 distance: 112 - 117: 26.210 distance: 114 - 115: 37.644 distance: 115 - 116: 26.380 distance: 117 - 118: 50.216 distance: 118 - 119: 52.038 distance: 118 - 121: 56.902 distance: 119 - 120: 11.585 distance: 119 - 125: 49.274 distance: 121 - 122: 27.782 distance: 121 - 123: 21.307 distance: 122 - 124: 9.655 distance: 125 - 126: 6.447 distance: 126 - 127: 50.633 distance: 126 - 129: 32.009 distance: 127 - 128: 24.815 distance: 127 - 134: 24.598 distance: 129 - 130: 23.903 distance: 130 - 131: 34.228 distance: 131 - 132: 11.066 distance: 131 - 133: 7.989